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Aleyasin SA, Moradi A, Abolhasani N, Abdollahi M. Investigating FGFR2 gene as a blood-based epigenetic biomarker in gastric cancer. Mol Biol Rep 2024; 51:253. [PMID: 38302798 DOI: 10.1007/s11033-023-09082-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/30/2023] [Indexed: 02/03/2024]
Abstract
BACKGROUND Gastric adenocarcinoma is a prevalent form of cancer that often remains undetected in its early stages due to the lack of specific symptoms. This delayed diagnosis leads to poor clinical outcomes, underscoring the need for an effective and non-invasive method for early detection. Recent advances in cancer epigenetics have led to the identification of biomarkers that have the potential to revolutionize the early detection and monitoring of this disease. One such promising biomarker is the methylation of the FGFR2 promoter. This study aims to measure the methylation levels of a specific CpG site in the FGFR2 promoter gene in DNA extracted from blood leukocytes from patients with intestinal metaplasia, gastric cancer, and healthy control. MATERIAL AND METHODS The CpG site of the FGFR2 gene promoter was identified in its control region. Methylation alteration of the selected FGFR2 CpG site was determined through the (methylation-sensitive restriction enzyme) MSRE-qPCR. Genomic DNA was extracted from one hundred twenty-five participants. RESULTS The normal group had mean methylation levels of 93.23 ± 4.929%, while the IM group had a level of 69.85 ± 27.15%. In GC patients, the levels varied, with 25.96 ± 18.98% in the intestinal type and 28.30 ± 16.07% in the diffuse type. The methylation levels in the IM and GC patients were significantly lower than those in the normal control group. However, no significant difference was observed between the methylation status of the intestinal type of GC and the diffuse type. The Receiver operating characteristic (ROC) curve analysis showed that FGFR2 CpG methylation levels in GC patients compared to normal controls had a high sensitivity of 100% and specificity of 100%, with a cut-off of < 74.25%; when GC patients were compared to IM patients, the sensitivity was 85%, and the specificity was 80%, with a cut-off < 44.45%. CONCLUSIONS The potential of the FGFR2 methylation status as a non-invasive biomarker lies in its ability to be detected in blood leukocytes, which makes it a promising tool for the early detection of intestinal metaplasia and gastric cancer. This could significantly improve the detection and management of these gastric conditions.
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Affiliation(s)
- Seyed Ahmad Aleyasin
- Department of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), 17 Km Tehran-Karaj Highway, Pajoohesh Blvd, Tehran, Iran.
| | - Arash Moradi
- Department of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), 17 Km Tehran-Karaj Highway, Pajoohesh Blvd, Tehran, Iran
| | - Naeimeh Abolhasani
- Department of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), 17 Km Tehran-Karaj Highway, Pajoohesh Blvd, Tehran, Iran
| | - Mahvash Abdollahi
- Department of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), 17 Km Tehran-Karaj Highway, Pajoohesh Blvd, Tehran, Iran
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Creighton CJ, Zhang F, Zhang Y, Castro P, Hu R, Islam M, Ghosh S, Ittmann M, Kwabi-Addo B. Comparative and integrative analysis of transcriptomic and epigenomic-wide DNA methylation changes in African American prostate cancer. Epigenetics 2023; 18:2180585. [PMID: 37279148 PMCID: PMC9980641 DOI: 10.1080/15592294.2023.2180585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 02/01/2023] [Indexed: 02/24/2023] Open
Abstract
African American (AA) men have the highest incidence and mortality rate from Prostate cancer (PCa) than any other racial/ethnic group. To date, PCa genomic studies have largely under-represented tumour samples from AA men. We measured genome-wide DNA methylation in benign and tumor prostate tissues from AA men using the Illumina Infunium 850 K EPIC array. mRNA expression database from a subset of the AA biospecimen were used to assess correlation of transcriptome and methylation datasets. Genome-wide methylation analysis identified 11,460 probes that were significant (p < 0.01) and differentially methylated in AA PCa compared to normal prostate tissues and showed significant (p < 0.01) inverse-correlation with mRNA expression. Ingenuity pathway analysis and Gene Ontology analysis in our AA dataset compared with TCGA dataset showed similarities in methylation patterns: top candidate genes with significant hypermethylation and corresponding down-regulated gene expression were associated with biological pathways in hemidesmosome assembly, mammary gland development, epidermis development, hormone biosynthesis, and cell communication. In addition, top candidate genes with significant hypomethylation and corresponding up-regulated gene expression were associated with biological pathways in macrophage differentiation, cAMP-dependent protein kinase activity, protein destabilization, transcription co-repression, and fatty acid biosynthesis. In contrast, differences in genome-wide methylation in our AA dataset compared with TCGA dataset were enriched for genes in steroid signalling, immune signalling, chromatin structure remodelling and RNA processing. Overall, differential methylation of AMIGO3, IER3, UPB1, GRM7, TFAP2C, TOX2, PLSCR2, ZNF292, ESR2, MIXL1, BOLL, and FGF6 were significant and uniquely associated with PCa progression in our AA cohort.
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Affiliation(s)
- Chad J. Creighton
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Flora Zhang
- Center for Women’s Studies, Colgate University, Hamilton, New York, USA
| | - Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Patricia Castro
- Department of Pathology and Immunology, Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas, USA
| | - Rong Hu
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA
| | - Md Islam
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA
| | - Somiranjan Ghosh
- Department of Biology, Howard University, Washington, Columbia, USA
| | - Michael Ittmann
- Department of Pathology and Immunology, Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas, USA
| | - Bernard Kwabi-Addo
- Department of Biochemistry and Molecular Biology, Howard University, Washington, Columbia, USA
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Shoukat I, Mueller CR. Searching for DNA methylation in patients triple-negative breast cancer: a liquid biopsy approach. Expert Rev Mol Diagn 2023; 23:41-51. [PMID: 36715539 DOI: 10.1080/14737159.2023.2173579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
INTRODUCTION Liquid biopsies are proving to have diagnostic and prognostic value in many different cancers, and in breast cancer they have the potential to improve outcomes by providing valuable information throughout a patient's cancer journey. However, patients with triple negative breast cancer (TNBC) have received little benefit from such liquid biopsies due to underlying limitations in the discovery and utility of robust biomarkers. Here, we examine the development of DNA methylation-based liquid biopsy assays for breast cancer and how they pertain to TNBC. AREAS COVERED We conducted a systematic review of liquid biopsy assays for breast cancer and analyzed their relevance in TNBC. We show that the utility of DNA mutation-based assays is poor for TNBC due to the low mutational frequencies across the genome in this subtype. We offer a detailed review of mDETECT - a liquid biopsy specifically designed for assessing tumor burden in TNBC patients. EXPERT OPINION DNA methylation are foundational and robust events that occur in cancer evolution and may differentiate almost all forms of cancer, including TNBC. Longitudinal patient monitoring using DNA methylation-based liquid biopsies offers great potential for improving the detection and management of TNBC.
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Affiliation(s)
- Irsa Shoukat
- Queen's Cancer Research Institute, Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Christopher R Mueller
- Queen's Cancer Research Institute, Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
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4
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Khan H, Shah MR, Barek J, Malik MI. Cancer biomarkers and their biosensors: A comprehensive review. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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5
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DeLouize AM, Eick G, Karam SD, Snodgrass JJ. Current and future applications of biomarkers in samples collected through minimally invasive methods for cancer medicine and population-based research. Am J Hum Biol 2022; 34:e23665. [PMID: 34374148 PMCID: PMC9894104 DOI: 10.1002/ajhb.23665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 02/04/2023] Open
Abstract
Despite advances in cancer medicine and research, invasive and potentially risky procedures such as biopsies, venous blood tests, imaging, colonoscopy, and pap smear tests are still primarily used for screening, staging, and assessing response to therapy. The development and interdisciplinary use of biomarkers from urine, feces, saliva, scent, and capillary blood collected with minimally invasive methods represents a potential opportunity for integration with biomarker analysis for cancers, both in clinical practice (e.g., in screening, treatment, and disease monitoring, and improved quality of life for patients) and population-based research (e.g., in epidemiology/public health, studies of social and environmental determinants, and evolutionary medicine). In this article, we review the scientific rationale, benefits, challenges, and potential opportunities for measuring cancer-related biomarkers in samples collected through minimally invasive methods.
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Affiliation(s)
| | - Geeta Eick
- Department of Anthropology, University of Oregon, Eugene, Oregon, USA
| | - Sana D. Karam
- Department of Radiation Oncology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - J. Josh Snodgrass
- Department of Anthropology, University of Oregon, Eugene, Oregon, USA
- Center for Global Health, University of Oregon, Eugene, Oregon, USA
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6
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Albulescu A, Plesa A, Fudulu A, Iancu IV, Anton G, Botezatu A. Epigenetic approaches for cervical neoplasia screening (Review). Exp Ther Med 2021; 22:1481. [PMID: 34765022 PMCID: PMC8576616 DOI: 10.3892/etm.2021.10916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/27/2021] [Indexed: 02/07/2023] Open
Abstract
Human papillomavirus (HPV) infection is the leading cause of cervical cancer. The Papanicolaou cytology test is the usually employed type of screening for this infection; however, its sensibility is limited. Only a small percentage of women infected with high-risk HPV develop cervical cancer with an array of genetic and epigenetic modifications. Thus, it is necessary to develop rapid, reproducible and minimally invasive technologies for screening. DNA methylation has gained attention as an alternative method for molecular diagnosis and prognosis in HPV infection. The aim of the present review was to highlight the potential of DNA methylation in cervical neoplasia screening for clinical applications. It was observed that the methylation human and viral genes was correlated with high-grade lesions and cancer. Methylation biomarkers have shown a good capacity to discriminate between high-grade lesions with a transformative potential and cervical cancer, being able to detect these modifications at an early stage. With further research, the epigenetic profiles and subtypes of the tumors could be elaborated, which would aid in therapy selection by opening avenues in personalized precision medicine. Response to therapy could also be evaluated through such methods and the accessibility of liquid biopsies would allow a constant monitoring of the patient's status without invasive sampling techniques.
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Affiliation(s)
- Adrian Albulescu
- Department of Molecular Virology, Stefan S. Nicolau Institute of Virology, Bucharest 030304, Romania.,Pharmacology Department, National Institute for Chemical Pharmaceutical Research and Development, Bucharest 031299, Romania
| | - Adriana Plesa
- Department of Molecular Virology, Stefan S. Nicolau Institute of Virology, Bucharest 030304, Romania
| | - Alina Fudulu
- Department of Molecular Virology, Stefan S. Nicolau Institute of Virology, Bucharest 030304, Romania
| | - Iulia Virginia Iancu
- Department of Molecular Virology, Stefan S. Nicolau Institute of Virology, Bucharest 030304, Romania
| | - Gabriela Anton
- Department of Molecular Virology, Stefan S. Nicolau Institute of Virology, Bucharest 030304, Romania
| | - Anca Botezatu
- Department of Molecular Virology, Stefan S. Nicolau Institute of Virology, Bucharest 030304, Romania
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Mukherjee S, Dasgupta S, Mishra PK, Chaudhury K. Air pollution-induced epigenetic changes: disease development and a possible link with hypersensitivity pneumonitis. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:55981-56002. [PMID: 34498177 PMCID: PMC8425320 DOI: 10.1007/s11356-021-16056-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/16/2021] [Indexed: 05/16/2023]
Abstract
Air pollution is a serious threat to our health and has become one of the major causes of many diseases including cardiovascular disease, respiratory disease, and cancer. The association between air pollution and various diseases has long been a topic of research interest. However, it remains unclear how air pollution actually impacts health by modulating several important cellular functions. Recently, some evidence has emerged about air pollution-induced epigenetic changes, which are linked with the etiology of various human diseases. Among several epigenetic modifications, DNA methylation represents the most prominent epigenetic alteration underlying the air pollution-induced pathogenic mechanism. Several other types of epigenetic changes, such as histone modifications, miRNA, and non-coding RNA expression, have also been found to have been linked with air pollution. Hypersensitivity pneumonitis (HP), one of the most prevalent forms of interstitial lung diseases (ILDs), is triggered by the inhalation of certain organic and inorganic substances. HP is characterized by inflammation in the tissues around the lungs' airways and may lead to irreversible lung scarring over time. This review, in addition to other diseases, attempts to understand whether certain pollutants influence HP development through such epigenetic modifications.
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Affiliation(s)
- Suranjana Mukherjee
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India.
| | - Sanjukta Dasgupta
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Pradyumna K Mishra
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, Madhya Pradesh, 462030, India
| | - Koel Chaudhury
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
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Palanca-Ballester C, Rodriguez-Casanova A, Torres S, Calabuig-Fariñas S, Exposito F, Serrano D, Redin E, Valencia K, Jantus-Lewintre E, Diaz-Lagares A, Montuenga L, Sandoval J, Calvo A. Cancer Epigenetic Biomarkers in Liquid Biopsy for High Incidence Malignancies. Cancers (Basel) 2021; 13:cancers13123016. [PMID: 34208598 PMCID: PMC8233712 DOI: 10.3390/cancers13123016] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 06/04/2021] [Accepted: 06/11/2021] [Indexed: 02/07/2023] Open
Abstract
Early alterations in cancer include the deregulation of epigenetic events such as changes in DNA methylation and abnormal levels of non-coding (nc)RNAs. Although these changes can be identified in tumors, alternative sources of samples may offer advantages over tissue biopsies. Because tumors shed DNA, RNA, and proteins, biological fluids containing these molecules can accurately reflect alterations found in cancer cells, not only coming from the primary tumor, but also from metastasis and from the tumor microenvironment (TME). Depending on the type of cancer, biological fluids encompass blood, urine, cerebrospinal fluid, and saliva, among others. Such samples are named with the general term "liquid biopsy" (LB). With the advent of ultrasensitive technologies during the last decade, the identification of actionable genetic alterations (i.e., mutations) in LB is a common practice to decide whether or not targeted therapy should be applied. Likewise, the analysis of global or specific epigenetic alterations may also be important as biomarkers for diagnosis, prognosis, and even for cancer drug response. Several commercial kits that assess the DNA promoter methylation of single genes or gene sets are available, with some of them being tested as biomarkers for diagnosis in clinical trials. From the tumors with highest incidence, we can stress the relevance of DNA methylation changes in the following genes found in LB: SHOX2 (for lung cancer); RASSF1A, RARB2, and GSTP1 (for lung, breast, genitourinary and colon cancers); and SEPT9 (for colon cancer). Moreover, multi-cancer high-throughput methylation-based tests are now commercially available. Increased levels of the microRNA miR21 and several miRNA- and long ncRNA-signatures can also be indicative biomarkers in LB. Therefore, epigenetic biomarkers are attractive and may have a clinical value in cancer. Nonetheless, validation, standardization, and demonstration of an added value over the common clinical practice are issues needed to be addressed in the transfer of this knowledge from "bench to bedside".
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Affiliation(s)
- Cora Palanca-Ballester
- Biomarkers and Precision Medicine (UBMP) and Epigenomics Unit, IIS, La Fe, 46026 Valencia, Spain;
| | - Aitor Rodriguez-Casanova
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, Spain; (A.R.-C.); (A.D.-L.)
- Roche-CHUS Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), 15706 Santiago de Compostela, Spain
| | - Susana Torres
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, 46014 Valencia, Spain
- TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación para la Investigación del Hospital General Universitario de Valencia, 46014 Valencia, Spain
| | - Silvia Calabuig-Fariñas
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, 46014 Valencia, Spain
- TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación para la Investigación del Hospital General Universitario de Valencia, 46014 Valencia, Spain
- Department of Pathology, Universitat de València, 46010 Valencia, Spain
| | - Francisco Exposito
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Diego Serrano
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Esther Redin
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Karmele Valencia
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Biochemistry and Genetics, School of Sciences, University of Navarra, 31008 Pamplona, Spain
| | - Eloisa Jantus-Lewintre
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, 46014 Valencia, Spain
- TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación para la Investigación del Hospital General Universitario de Valencia, 46014 Valencia, Spain
- Department of Biotechnology, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Angel Diaz-Lagares
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, Spain; (A.R.-C.); (A.D.-L.)
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
| | - Luis Montuenga
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Juan Sandoval
- Biomarkers and Precision Medicine (UBMP) and Epigenomics Unit, IIS, La Fe, 46026 Valencia, Spain;
- Correspondence: (J.S.); (A.C.)
| | - Alfonso Calvo
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
- Correspondence: (J.S.); (A.C.)
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Rubio-Ramos A, Labat-de-Hoz L, Correas I, Alonso MA. The MAL Protein, an Integral Component of Specialized Membranes, in Normal Cells and Cancer. Cells 2021; 10:1065. [PMID: 33946345 PMCID: PMC8145151 DOI: 10.3390/cells10051065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/12/2022] Open
Abstract
The MAL gene encodes a 17-kDa protein containing four putative transmembrane segments whose expression is restricted to human T cells, polarized epithelial cells and myelin-forming cells. The MAL protein has two unusual biochemical features. First, it has lipid-like properties that qualify it as a member of the group of proteolipid proteins. Second, it partitions selectively into detergent-insoluble membranes, which are known to be enriched in condensed cell membranes, consistent with MAL being distributed in highly ordered membranes in the cell. Since its original description more than thirty years ago, a large body of evidence has accumulated supporting a role of MAL in specialized membranes in all the cell types in which it is expressed. Here, we review the structure, expression and biochemical characteristics of MAL, and discuss the association of MAL with raft membranes and the function of MAL in polarized epithelial cells, T lymphocytes, and myelin-forming cells. The evidence that MAL is a putative receptor of the epsilon toxin of Clostridium perfringens, the expression of MAL in lymphomas, the hypermethylation of the MAL gene and subsequent loss of MAL expression in carcinomas are also presented. We propose a model of MAL as the organizer of specialized condensed membranes to make them functional, discuss the role of MAL as a tumor suppressor in carcinomas, consider its potential use as a cancer biomarker, and summarize the directions for future research.
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Affiliation(s)
- Armando Rubio-Ramos
- Centro de Biología Molecular “Severo Ochoa”, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, 28049 Madrid, Spain; (A.R.-R.); (L.L.-d.-H.); (I.C.)
| | - Leticia Labat-de-Hoz
- Centro de Biología Molecular “Severo Ochoa”, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, 28049 Madrid, Spain; (A.R.-R.); (L.L.-d.-H.); (I.C.)
| | - Isabel Correas
- Centro de Biología Molecular “Severo Ochoa”, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, 28049 Madrid, Spain; (A.R.-R.); (L.L.-d.-H.); (I.C.)
- Department of Molecular Biology, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Miguel A. Alonso
- Centro de Biología Molecular “Severo Ochoa”, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, 28049 Madrid, Spain; (A.R.-R.); (L.L.-d.-H.); (I.C.)
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10
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Yao Y, Xu P, Ying T, Wang Y, Wang X, Shu L, Mo Z, Chen Z, Wang X, Wang W, Teng L, Lou X. Integrative Analysis of DNA Methylation and Gene Expression Identified Follicular Thyroid Cancer-Specific Diagnostic Biomarkers. Front Endocrinol (Lausanne) 2021; 12:736068. [PMID: 35370931 PMCID: PMC8964406 DOI: 10.3389/fendo.2021.736068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 10/21/2021] [Indexed: 12/15/2022] Open
Abstract
The diagnosis of follicular thyroid carcinoma (FTC) prior surgical resection remains a challenge, as routine screening methods, such as ultrasound or even FNAB, could not diagnose FTC preoperatively. Here, we performed an integrative analysis of DNA methylation and RNA array data from our own cohort (14 Follicular thyroid carcinoma vs 16 Benign thyroid lesion) to identify thyroid cancer-specific DNA methylation markers. We first identified differentially methylated and expressed genes and examined their correlations. Candidate DNA methylation sites were selected and further verified in validation set. Among all candidate methylation sites, cg06928209 was the most promising site as a molecular marker for early diagnosis, with a sensitivity of 90%, a specificity of 80% and an AUC of 0.77. Overall, our study demonstrates the potential use of methylation markers in FTC diagnosis and may boost the development of new epigenetic therapies.
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Affiliation(s)
- Yunjin Yao
- Department of Surgical Oncology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Peiwei Xu
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Tianxing Ying
- Department of Surgical Oncology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yue Wang
- Department of Surgical Oncology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xumeng Wang
- Department of Surgical Oncology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Liqi Shu
- Warren Alpert School of Medicine, Brown University, Providence, RI, United States
| | - Zhe Mo
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Zhijian Chen
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Xiaofeng Wang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Weibin Wang
- Department of Surgical Oncology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- *Correspondence: Xiaoming Lou, ; Lisong Teng, ; Weibin Wang,
| | - Lisong Teng
- Department of Surgical Oncology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- *Correspondence: Xiaoming Lou, ; Lisong Teng, ; Weibin Wang,
| | - Xiaoming Lou
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
- *Correspondence: Xiaoming Lou, ; Lisong Teng, ; Weibin Wang,
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Gobbini E, Swalduz A, Giaj Levra M, Ortiz-Cuaran S, Toffart AC, Pérol M, Moro-Sibilot D, Saintigny P. Implementing ctDNA Analysis in the Clinic: Challenges and Opportunities in Non-Small Cell Lung Cancer. Cancers (Basel) 2020; 12:E3112. [PMID: 33114393 PMCID: PMC7693855 DOI: 10.3390/cancers12113112] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/21/2020] [Accepted: 10/21/2020] [Indexed: 12/14/2022] Open
Abstract
Tumor genomic profiling has a dramatic impact on the selection of targeted treatment and for the identification of resistance mechanisms at the time of progression. Solid tissue biopsies are sometimes challenging, and liquid biopsies are used as a non-invasive alternative when tissue is limiting. The clinical relevance of tumor genotyping through analysis of ctDNA is now widely recognized at all steps of the clinical evaluation process in metastatic non-small cell lung cancer (NSCLC) patients. ctDNA analysis through liquid biopsy has recently gained increasing attention as well in the management of early and locally advanced, not oncogene-addicted, NSCLC. Its potential applications in early disease detection and the response evaluation to radical treatments are promising. The aim of this review is to summarize the landscape of liquid biopsies in clinical practice and also to provide an overview of the potential perspectives of development focusing on early detection and screening, the assessment of minimal residual disease, and its potential role in predicting response to immunotherapy. In addition to available studies demonstrating the clinical relevance of liquid biopsies, there is a need for standardization and well-designed clinical trials to demonstrate its clinical utility.
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Affiliation(s)
- Elisa Gobbini
- Thoracic Oncology Unit, CHU Grenoble-Alpes, 38700 Grenoble, France or (E.G.); (M.G.L.); (A.-C.T.); (D.M.-S.)
- Univ Lyon, Université Claude Bernard Lyon, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69373 Lyon, France; (S.O.-C.)
| | - Aurélie Swalduz
- Department of Medical Oncology, Centre Léon Bérard, 69373 Lyon, France; (A.S.); (M.P.)
| | - Matteo Giaj Levra
- Thoracic Oncology Unit, CHU Grenoble-Alpes, 38700 Grenoble, France or (E.G.); (M.G.L.); (A.-C.T.); (D.M.-S.)
| | - Sandra Ortiz-Cuaran
- Univ Lyon, Université Claude Bernard Lyon, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69373 Lyon, France; (S.O.-C.)
| | - Anne-Claire Toffart
- Thoracic Oncology Unit, CHU Grenoble-Alpes, 38700 Grenoble, France or (E.G.); (M.G.L.); (A.-C.T.); (D.M.-S.)
| | - Maurice Pérol
- Department of Medical Oncology, Centre Léon Bérard, 69373 Lyon, France; (A.S.); (M.P.)
| | - Denis Moro-Sibilot
- Thoracic Oncology Unit, CHU Grenoble-Alpes, 38700 Grenoble, France or (E.G.); (M.G.L.); (A.-C.T.); (D.M.-S.)
| | - Pierre Saintigny
- Univ Lyon, Université Claude Bernard Lyon, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69373 Lyon, France; (S.O.-C.)
- Department of Medical Oncology, Centre Léon Bérard, 69373 Lyon, France; (A.S.); (M.P.)
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12
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Bagheri H, Mosallaei M, Bagherpour B, Khosravi S, Salehi AR, Salehi R. TFPI2 and NDRG4 gene promoter methylation analysis in peripheral blood mononuclear cells are novel epigenetic noninvasive biomarkers for colorectal cancer diagnosis. J Gene Med 2020; 22:e3189. [PMID: 32196834 DOI: 10.1002/jgm.3189] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 03/11/2020] [Accepted: 03/12/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND As a result of the growing prevalence of colorectal cancer (CRC), new screening and early detection methods are required. Among the novel biomarkers, DNA methylation has emerged as a high-potential diagnosis/screening molecular marker. The present study aimed to assess non-invasive early diagnosis of CRC by examining promoter methylation of TFPI2 and NDRG4 genes in peripheral blood mononuclear cells (PBMCs). METHODS Fifty CRC patients and 50 normal controls were recruited to the present study. Quantitative methylation of the promoter region of the TFPI2 and NDRG4 genes was analyzed in DNA extracted from PBMCs of all cases and control subjects using a methylation-quantification endonuclease-resistant DNA (MethyQESD) method. RESULTS The sensitivity and specificity of the TFPI2 gene for the diagnosis of CRC was 88% and 92%, respectively, and, for the NDRG4 gene, it was 86% and 92%, respectively. The methylation range for the TFPI2 gene was 43.93% and 11.56% in patients and controls, respectively, and, for the NDRG4 gene, it was 38.8% in CRC patients and 12.23% in healthy controls (p < 0.001). In addition, we observed that a higher percentage of methylation was correlated with the higher stage of CRC. CONCLUSIONS The results of the present study reveal that PBMCs are reliable sources of methylation analysis for CRC screening. Furthermore, the TFPI2 and NDRG4 genes provide sufficiently high sensitivity and specificity to be nominated for use in a novel noninvasive CRC screening method in PBMCs.
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Affiliation(s)
- Hadi Bagheri
- Department of Genetics and Molecular biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Meysam Mosallaei
- Department of Genetics and Molecular biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Bahram Bagherpour
- Department of Genetics and Molecular biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.,Gerfa Namayesh Azmayesh (GENAZMA) Science & Research Institute, Isfahan, Iran
| | - Sharifeh Khosravi
- Department of Genetics and Molecular biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ahmad Reza Salehi
- Department of Genetics and Molecular biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Rasoul Salehi
- Department of Genetics and Molecular biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.,Gerfa Namayesh Azmayesh (GENAZMA) Science & Research Institute, Isfahan, Iran
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13
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Zang R, Wang X, Jin R, Lei Y, Huang J, Liu C, Zheng S, Zhou F, Wu Q, Sun N, Gao S, He J. Translational value of IDH1 and DNA methylation biomarkers in diagnosing lung cancers: a novel diagnostic panel of stage and histology-specificity. J Transl Med 2019; 17:430. [PMID: 31888670 PMCID: PMC6936123 DOI: 10.1186/s12967-019-2117-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 10/26/2019] [Indexed: 12/24/2022] Open
Abstract
Background Lung cancer is the leading cause of cancer-related death worldwide, and the timely and serial assessment of low-dose computed tomography (LDCT) in high-risk populations remains a challenge. Furthermore, testing a single biomarker for the diagnosis of lung cancers is of relatively low effectiveness. Thus, a stronger diagnostic combination of blood biomarkers is needed to improve the diagnosis of non-small cell lung cancer (NSCLC). Methods The blood levels of individual biomarkers [IDH1, DNA methylation of short stature homeobox 2 gene (SHOX2), and prostaglandin E receptor 4 gene (PTGER4)] were measured and statistically analyzed in samples from healthy controls and patients with lung cancer. In total, 221 candidates were enrolled and randomly assigned into two groups for the training and validation of a diagnostic panel. Additionally, a subgroup analysis was performed in the whole cohort. Results A newly combined 3-marker diagnostic model for lung cancers was established and validated with area under the receiver operating characteristic (ROC) curve (AUC) values ranging from 0.835 to 0.905 in independent groups showing significantly stronger diagnostic value compared with a single tested biomarker. The sensitivity of the diagnostic model was as high as 86.1% and 80.0% in the training and validation sets, respectively. Although no apparent differences were found between the 3-marker and 2-marker models, the high clinical T-stage and histological type specificity of IDH1 and two other methylated DNA biomarkers were demonstrated in the subgroup analysis. Conclusions The combination of single biomarkers with high stage-specificity and histological type specificity (SHOX2 and PTGER4 DNA methylation and IDH1) showed better diagnostic performance in the detection of lung cancers compared with single marker assessment. A greater clinical utility of the panel may be developed by adding demographic/epidemiologic characteristics.
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Affiliation(s)
- Ruochuan Zang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xinfeng Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Runsen Jin
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yuanyuan Lei
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jianbing Huang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Chengming Liu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Sufei Zheng
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Fang Zhou
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Qian Wu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Nan Sun
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Shugeng Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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14
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Zheng H, Wu X, Yin J, Wang S, Li Z, You C. Clinical applications of liquid biopsies for early lung cancer detection. Am J Cancer Res 2019; 9:2567-2579. [PMID: 31911847 PMCID: PMC6943362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 11/15/2019] [Indexed: 06/10/2023] Open
Abstract
Over the past decade, the clinical utility of liquid biopsies in lung cancer has drawn increasing attention. Having been successfully applied in targeted therapy for late stage lung cancer, liquid biopsies are being further investigated regarding their potential role for early detection of lung cancer. Novel biomarkers with high sensitivity and specificity are crucial for identifying patients at early stages as well as for monitoring high-risk populations. A variety of bodily fluids (such as plasma, serum, and sputum) and biomarkers (such as cfDNA, CTCs, gene methylation, and miRNA) have been investigated for their potential role in the diagnosis of lung cancer. In this review, we summarize recent advances in circulating biomarkers regarding the early detection of lung cancer and discuss their potential applications and challenges in clinical settings.
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Affiliation(s)
- Hao Zheng
- Department of Bioinformatics, Lianxi Biotech800 HuanHu Xier Road, Shanghai, China
- Department of Bioinformatics, Novo Vivo Inc435 Tasso St, Palo Alto, CA 94301, USA
| | - Xin Wu
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Second Military Medical UniversityShanghai, China
| | - Jie Yin
- Purdue University625 Agriculture Mall Dr, West Lafayette, IN 47907, USA
| | - Shuang Wang
- School of Informatics, Computing and Engineering, Indiana University BloomingtonBloomington, IN 47405, USA
- Institutes for Systems Genetics, West China HospitalChengdu, Sichuan, China
- Shanghai Putuo People’s Hospital, Tongji UniversityShanghai, China
- Department of Bioinformatics, Novo Vivo Inc435 Tasso St, Palo Alto, CA 94301, USA
| | - Zhi Li
- Department of Bioinformatics, Lianxi Biotech800 HuanHu Xier Road, Shanghai, China
| | - Changxuan You
- Department of Oncology, Medical Center for Overseas Patient, Nanfang Hospital, Southern Medical UniversityGuangzhou, China
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15
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Ibrahim J, Op de Beeck K, Fransen E, Peeters M, Van Camp G. The Gasdermin E Gene Has Potential as a Pan-Cancer Biomarker, While Discriminating between Different Tumor Types. Cancers (Basel) 2019; 11:cancers11111810. [PMID: 31752152 PMCID: PMC6896019 DOI: 10.3390/cancers11111810] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/04/2019] [Accepted: 11/06/2019] [Indexed: 01/08/2023] Open
Abstract
Due to the elevated rates of incidence and mortality of cancer, early and accurate detection is crucial for achieving optimal treatment. Molecular biomarkers remain important screening and detection tools, especially in light of novel blood-based assays. DNA methylation in cancer has been linked to tumorigenesis, but its value as a biomarker has not been fully explored. In this study, we have investigated the methylation patterns of the Gasdermin E gene across 14 different tumor types using The Cancer Genome Atlas (TCGA) methylation data (N = 6502). We were able to identify six CpG sites that could effectively distinguish tumors from normal samples in a pan-cancer setting (AUC = 0.86). This combination of pan-cancer biomarkers was validated in six independent datasets (AUC = 0.84–0.97). Moreover, we tested 74,613 different combinations of six CpG probes, where we identified tumor-specific signatures that could differentiate one tumor type versus all the others (AUC = 0.79–0.98). In all, methylation patterns exhibited great variation between cancer and normal tissues, but were also tumor specific. Our analyses highlight that a Gasdermin E methylation biomarker assay, not only has the potential for being a methylation-specific pan-cancer detection marker, but it also possesses the capacity to discriminate between different types of tumors.
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Affiliation(s)
- Joe Ibrahim
- Centre of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650 Edegem, Belgium; (J.I.); (K.O.d.B.); (E.F.)
- Centre for Oncological Research, University of Antwerp and Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium;
| | - Ken Op de Beeck
- Centre of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650 Edegem, Belgium; (J.I.); (K.O.d.B.); (E.F.)
- Centre for Oncological Research, University of Antwerp and Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium;
| | - Erik Fransen
- Centre of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650 Edegem, Belgium; (J.I.); (K.O.d.B.); (E.F.)
- StatUa Centre for Statistics, University of Antwerp, 2000 Antwerp, Belgium
| | - Marc Peeters
- Centre for Oncological Research, University of Antwerp and Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium;
- Department of Medical Oncology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium
| | - Guy Van Camp
- Centre of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650 Edegem, Belgium; (J.I.); (K.O.d.B.); (E.F.)
- Centre for Oncological Research, University of Antwerp and Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium;
- Correspondence: ; Tel.: +32-3275-9762
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Barros-Filho MC, Dos Reis MB, Beltrami CM, de Mello JBH, Marchi FA, Kuasne H, Drigo SA, de Andrade VP, Saieg MA, Pinto CAL, Kowalski LP, Rogatto SR. DNA Methylation-Based Method to Differentiate Malignant from Benign Thyroid Lesions. Thyroid 2019; 29:1244-1254. [PMID: 31328658 DOI: 10.1089/thy.2018.0458] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Background: The differential diagnosis of thyroid nodules using fine-needle aspiration biopsy (FNAB) is challenging due to the inherent limitation of the cytology tests. The use of molecular markers has potential to complement the FNAB-based diagnosis and avoid unnecessary surgeries. In this study, we aimed to identify DNA methylation biomarkers and to develop a diagnostic tool useful for thyroid lesions. Methods: Genome-wide DNA methylation profiles (Illumina 450K) of papillary thyroid carcinoma (PTC = 60) and follicular thyroid carcinoma (FTC = 10) were compared with non-neoplastic thyroid tissue samples (NT = 50) and benign thyroid lesions (BTL = 17). The results were confirmed in publicly available databases from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) using the same DNA methylation platform. Two classifiers were trained to discriminate FTC and PTC from BTL. To increase the applicability of the method, six differentially methylated CpGs were selected and evaluated in 161 thyroid tumors and 69 BTL postsurgical specimens and 55 prospectively collected FNAB using bisulfite-pyrosequencing. Results: DNA methylation analysis revealed 2130 and 19 differentially methylated CpGs in PTC and FTC, respectively. The CpGs confirmed by GEO and TCGA databases showing high areas under the receiver operating characteristic curve in all sample sets were used to train our diagnostic classifier. The model based on six CpGs was able to differentiate benign from malignant thyroid lesions with 94.3% sensitivity and 82.4% specificity. A similar performance was found applying the algorithm to TCGA and GEO external data sets (91.3-97.4% sensitivity and 87.5% specificity). We successfully evaluated the classifiers using a bisulfite-pyrosequencing technique, achieving 90.7% sensitivity and 75.4% specificity in surgical specimens (five of six CpGs). The study comprising FNAB cytology materials corroborated the applicability and performance of the methodology, demonstrating 86.7% sensitivity and 89.5% specificity in confirmed malignant tumors, and 100% sensitivity and 89% specificity in cases with indeterminate cytology. Conclusions: A novel diagnostic tool with potential application in preoperative screening of thyroid nodules is reported here. The proposed protocol has the potential to avoid unnecessary thyroidectomies.
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Affiliation(s)
| | - Mariana Bisarro Dos Reis
- International Research Center - CIPE-A.C.Camargo Cancer Center, São Paulo, Brazil
- Faculty of Medicine, University of Sao Paulo State-UNESP, Botucatu, Brazil
| | | | | | | | - Hellen Kuasne
- International Research Center - CIPE-A.C.Camargo Cancer Center, São Paulo, Brazil
| | | | | | - Mauro Ajaj Saieg
- Department of Pathology, A.C.Camargo Cancer Center, São Paulo, Brazil
| | | | - Luiz Paulo Kowalski
- Department of Head and Neck Surgery and Otorhinolaryngology, A.C.Camargo Cancer Center, São Paulo, Brazil
| | - Silvia Regina Rogatto
- Department of Clinical Genetics, Vejle Hospital, Institute of Regional Health Research, University of Southern Denmark, Vejle, Denmark
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17
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Bi H, Liu Y, Pu R, Xia T, Sun H, Huang H, Zhang L, Zhang Y, Liu Y, Xu J, Rong J, Zhao Y. CHST7 Gene Methylation and Sex-Specific Effects on Colorectal Cancer Risk. Dig Dis Sci 2019; 64:2158-2166. [PMID: 30815821 DOI: 10.1007/s10620-019-05530-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 02/11/2019] [Indexed: 01/09/2023]
Abstract
BACKGROUND X chromosome aberrations are involved in carcinogenesis and are associated with gender differences in cancer development. Abnormal DNA methylation also contributes to cancer. Carbohydrate Sulfotransferase 7 (CHST7), encoded by the X chromosome, is abnormally expressed during tumor development. However, its impact on colorectal cancer (CRC) and the effect of CHST7 methylation on sex-specific CRC risk remain unclear. AIMS To investigate the effect of CHST7 methylation in white blood cells on CRC risk and to evaluate its impact on gender-specific differences. METHODS CHST7 methylation in white blood cells was determined using methylation-sensitive high-resolution melting. A propensity score analysis was performed to control potential confounders. Furthermore, extensive sensitivity analyses were applied to assess the robustness of our findings. In addition, we validated the initial findings with a GEO dataset (GSE51032). RESULTS CHST7 hypermethylation in white blood cells was associated with an increased CRC risk [odds ratio (OR)adj = 4.447, 95% confidence interval (CI) 2.662-7.430; p < 0.001]. The association was validated with the GEO dataset (ORadj = 2.802, 95% CI 1.235-6.360; p = 0.014). In particular, CHST7 hypermethylation significantly increased the CRC risk in females (ORadj = 7.704, 95% CI 4.222-14.058; p < 0.001) and younger patients (≤ 60 years) (ORadj = 5.755, 95% CI 2.540-13.038; p < 0.001). Subgroup analyses by tumor location and Duke's stage also observed these associations. CONCLUSION CHST7 methylation in white blood cells is positively associated with CRC risk, especially in females, and may potentially serve as a blood-based predictive biomarker for CRC risk.
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Affiliation(s)
- Haoran Bi
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Yupeng Liu
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Rui Pu
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Tingting Xia
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Hongru Sun
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Hao Huang
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Lei Zhang
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Yuanyuan Zhang
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Ying Liu
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Jing Xu
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Jiesheng Rong
- Department of Orthopedics Surgery, The Second Affiliated Hospital of Harbin Medical University, 246, Xuefu Street, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Yashuang Zhao
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150081, Heilongjiang Province, People's Republic of China.
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18
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Wu TH, Hsiue EHC, Yang JCH. Opportunities of circulating tumor DNA in lung cancer. Cancer Treat Rev 2019; 78:31-41. [PMID: 31326635 DOI: 10.1016/j.ctrv.2019.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/02/2019] [Accepted: 07/06/2019] [Indexed: 12/24/2022]
Abstract
Current classification and treatment of lung cancer rely increasingly on molecular and genetic testing. Obtaining tumor tissue is not always feasible and multiple biopsies are undesirable. In response to the demand for non-invasive molecular and genetic testing in cancer care, several liquid biopsy technologies, including circulating DNA (ctDNA), have been developed. ctDNA analysis is now technically feasible to be carried out in large scales and integrated into clinical practice owing to the advances in technology. Despite the challenges in improving test accuracy and cost-effectiveness, there are huge potentials for ctDNA analysis in lung cancer management. This review focuses on the clinical utility of ctDNA analysis in lung cancer, including early detection, monitoring treatment response and detecting residual disease, identification of genetic determinants for targeted therapy, and predicting efficacy of immune checkpoint blockade.
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Affiliation(s)
- Ting-Hui Wu
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, United States
| | | | - James Chih-Hsin Yang
- Department of Oncology, National Taiwan University Hospital, Taiwan; Graduate Institute of Oncology, National Taiwan University, Taiwan.
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19
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Wu J, Zhang Y, Li M. Identification of Methylation Markers and Differentially Expressed Genes with Prognostic Value in Breast Cancer. J Comput Biol 2019; 26:1394-1408. [PMID: 31290690 DOI: 10.1089/cmb.2019.0179] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Breast cancer is one of the most common cancers causing a high mortality worldwide. This study aimed to identify differential methylation and expression genes with prognostic value in breast cancer. DNA methylation and gene expression profiles (GSE60185, GSE42568, GSE21653, GSE58812, and GSE52865) were downloaded from TCGA (The Cancer Genome Atlas) and GEO (Gene Expression Omnibus) databases. The differentially expressed genes (DEGs) and differential methylation genes were identified between breast cancer samples and normal samples. Functional analysis was performed using DAVID (Database for Annotation, Visualization, and Integrated Discovery) tool. Furthermore, functional epigenetic modules (FEM) were analyzed to identify critical genes with prognostic values. A large amount of DEGs and aberrant methylation genes were identified between breast cancer samples and normal samples. These genes were mainly associated with several GO (Gene Ontology) terms and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, such as neuroactive ligand-receptor interaction, alcoholism, gamma-aminobutyric acid signaling pathway, and G-protein-coupled receptor signaling pathway. Additionally, 10 DEGs with differential methylation levels were significantly correlated with survival outcomes in breast cancer patients. FEM analysis revealed that several DEGs (e.g., GABRA4, GABRG1, and GABRA1) in module GABRA4 were identified as potential biomarkers in breast cancer patients. Several DEGs identified were associated with breast cancer prognosis. These DEGs might act as prognostic and diagnostic markers in breast cancer.
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Affiliation(s)
- Jie Wu
- Key Laboratory of Hydrodynamics (Ministry of Education), School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yijian Zhang
- Shanghai Research Center of Biliary Tract Disease, Shanghai, China.,Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China
| | - Maolan Li
- Shanghai Research Center of Biliary Tract Disease, Shanghai, China
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20
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Epiphanio TMF, Fernandes NCCDA, de Oliveira TF, Lopes PA, Réssio RA, Gonçalves S, Scattone NV, Tedardi MV, Kulikowski LD, Damasceno J, Loureiro APDM, Dagli MLZ. Global DNA methylation of peripheral blood leukocytes from dogs bearing multicentric non-Hodgkin lymphomas and healthy dogs: A comparative study. PLoS One 2019; 14:e0211898. [PMID: 30908498 PMCID: PMC6433272 DOI: 10.1371/journal.pone.0211898] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 01/22/2019] [Indexed: 12/31/2022] Open
Abstract
Non-Hodgkin lymphomas are among the most common types of tumors in dogs, and they are currently accepted as comparative models of the disease in humans. Aberrant patterns of DNA methylation seem to play a key role in the development of hematopoietic neoplasms in humans, constitute a special mechanism of transcriptional control, and may be influenced by genetic and environmental factors. Blood leukocyte DNA global methylation has been poorly investigated in dogs. The aim of this study is to examine whether peripheral blood global DNA methylation is associated with canine multicentric lymphomas. Peripheral venous blood samples from ten healthy dogs and nine dogs bearing multicentric lymphomas were collected, and the buffy coat was separated. Global DNA methylation was analyzed by High Performance Liquid Chromatography (HPLC) and immunocytochemistry (ICC). In both analyses, leukocytes from dogs with lymphoma presented lower global DNA methylation than in healthy dogs (HPLC: p = 0.027/ 5MeCyt immunoreactivity scores: p = 0.015). Moderate correlation was observed between the results obtained by HPLC and ICC (correlation coefficient = 0.50). For the identification of differently methylated genes between both groups, the Infinium Human Methylation (HM) EPIC BeadChip (850K) was used. Of the 853,307 CpGs investigated in the microarray, there were 34,574 probes hybridized in the canine samples. From this total, significant difference was observed in the methylation level of 8433 regions, and through the homologous and orthologous similarities 525 differently methylated genes were identified between the two groups. This study is pioneer in suggesting that dogs bearing non-Hodgkin lymphoma presented DNA global hypomethylation of circulating leukocytes compared with healthy dogs. Although canine samples were used in an assay developed specifically for human DNA, it was possible to identify differently methylated genes and our results reiterate the importance of the use of peripheral blood leukocytes in cancer research and possible new biomarkers targets.
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Affiliation(s)
| | | | - Tiago Franco de Oliveira
- Department of Pharmacoscience, Federal University of Health Sciences of Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | - Priscila Assis Lopes
- Veterinary Laboratory, Veterinary Image Institute, IVI, São Paulo, São Paulo, Brazil
| | | | - Simone Gonçalves
- Veterinary Hemotherapy Center, Hemovet, São Paulo, São Paulo, Brazil
| | - Náyra Villar Scattone
- Laboratory of Experimental and Comparative Oncology, Department of Pathology, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Marcello Vannucci Tedardi
- Laboratory of Experimental and Comparative Oncology, Department of Pathology, University of São Paulo, São Paulo, São Paulo, Brazil
| | | | - Jullian Damasceno
- Cytogenomic Laboratory, Department of Pathology, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Ana Paula de Melo Loureiro
- Department of Clinical and Toxicological Analysis, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Maria Lucia Zaidan Dagli
- Laboratory of Experimental and Comparative Oncology, Department of Pathology, University of São Paulo, São Paulo, São Paulo, Brazil
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Epigenetic Suppression of the T-box Subfamily 2 ( TBX2) in Human Non-Small Cell Lung Cancer. Int J Mol Sci 2019; 20:ijms20051159. [PMID: 30866410 PMCID: PMC6429281 DOI: 10.3390/ijms20051159] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/15/2019] [Accepted: 02/18/2019] [Indexed: 12/25/2022] Open
Abstract
(1) The TBX2 subfamily of transcription factors (TBXs 2, 3, 4 and 5) are markedly down-regulated in human non-small cell lung cancer (NSCLC) and exert tumor suppressor effects in lung malignancy. Yet, mechanisms underlying suppressed expression of the TBX2 subfamily in NSCLC are elusive. Here, we interrogated probable epigenetic mechanisms in suppressed expression of the TBX2 subfamily in human NSCLC. (2) TBX2 subfamily gene expression and methylation levels in NSCLC and normal lung tissues were surveyed using publicly available RNA-sequence and genome-wide methylation datasets. Methylation β-values of the four genes were statistically compared between NSCLCs and normal lung tissues, correlated with gene expression levels, and interrogated with clinicopathological variables. Expression and methylation levels of TBXs were quantified in NSCLC cells using real-time PCR and methylation-specific PCR assays, respectively. Effects of the DNA methyltransferase inhibitor 5-azacytidine (Aza) on TBX2 subfamily expression were assessed in NSCLC cells. Impact of TBX2 subfamily expression on Aza-treated cells was evaluated by RNA interference. (3) All four TBXs were significantly hypermethylated in NSCLCs relative to normal lung tissues (p < 0.05). Methylation β-values of the genes, with exception of TBX2, were significantly inversely correlated with corresponding mRNA expression levels (p < 0.05). We found no statistically significant differences in hypermethylation levels of the TBX2 subfamily by clinicopathological features including stage and tobacco history. Expression levels of the TBX genes were overall suppressed in NSCLC cells relative to normal alveolar cells. Members of the subfamily were significantly hypermethylated in all tested NSCLC cell lines relative to normal alveolar cells. Treatment with Aza induced the expression of the TBX2 subfamily concomitant with NSCLC cell growth inhibition. Further, simultaneous knockdown of the four TBX genes markedly reduced anti-growth effects of Aza in NSCLC cells. (4) Our study sheds light on new epigenetic profiles in the molecular pathogenesis of human NSCLC.
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Zhao H, Ma C, Yan Y, Chen M. A sensitive cyclic signal amplification fluorescence strategy for determination of methyltransferase activity based on graphene oxide and RNase H. J Mater Chem B 2019. [DOI: 10.1039/c9tb00743a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A sensitive fluorometric method for DNA methyltransferase activity detection based on graphene oxide and RNase H-assisted signal amplification.
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Affiliation(s)
- Han Zhao
- School of Life Sciences
- Central South University
- Changsha 410013
- China
| | - Changbei Ma
- School of Life Sciences
- Central South University
- Changsha 410013
- China
| | - Ying Yan
- School of Life Sciences
- Central South University
- Changsha 410013
- China
| | - Mingjian Chen
- School of Life Sciences
- Central South University
- Changsha 410013
- China
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23
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24
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Guarrera S, Viberti C, Cugliari G, Allione A, Casalone E, Betti M, Ferrante D, Aspesi A, Casadio C, Grosso F, Libener R, Piccolini E, Mirabelli D, Dianzani I, Magnani C, Matullo G. Peripheral Blood DNA Methylation as Potential Biomarker of Malignant Pleural Mesothelioma in Asbestos-Exposed Subjects. J Thorac Oncol 2018; 14:527-539. [PMID: 30408567 DOI: 10.1016/j.jtho.2018.10.163] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 10/02/2018] [Accepted: 10/27/2018] [Indexed: 12/19/2022]
Abstract
INTRODUCTION Malignant pleural mesothelioma (MPM) is an aggressive tumor strongly associated with asbestos exposure. Patients are usually diagnosed when current treatments have limited benefits, highlighting the need for noninvasive early diagnostic tests to monitor asbestos-exposed people. METHODS We used a genome-wide methylation array to identify, in asbestos-exposed subjects, novel blood DNA methylation markers of MPM in 163 MPM cases and 137 cancer-free controls (82 MPM cases and 68 controls, training set; replication in 81 MPM cases and 69 controls, test set) sampled from the same areas. RESULTS Evidence of differential methylation between MPM cases and controls was found (more than 800 cytosine-guanine dinucleotide sites, false discovery rate p value (pfdr) < 0.05), mainly in immune system-related genes. Considering the top differentially methylated signals, seven single- cytosine-guanine dinucleotides and five genomic regions of coordinated methylation replicated with similar effect size in the test set (pfdr < 0.05). The top hypomethylated single-CpG (cases versus controls effect size less than -0.15, pfdr < 0.05 in both the training and test sets) was detected in FOXK1 (Forkhead-box K1) gene, an interactor of BAP1 which was found mutated in MPM tissue and as germline mutation in familial MPM. In the test set, comparison of receiver operating characteristic curves and the area under the curve (AUC) of two models, including or excluding methylation, showed a significant increase in case/control discrimination when considering DNA methylation together with asbestos exposure (AUC = 0.81 versus AUC = 0.89, DeLong's test p = 0.0013). CONCLUSIONS We identified signatures of differential methylation in DNA from whole blood between asbestos exposed MPM cases and controls. Our results provide the rationale to further investigate, in prospective studies, the potential use of blood DNA methylation profiles for the identification of early changes related to the MPM carcinogenic process.
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Affiliation(s)
- Simonetta Guarrera
- Italian Institute for Genomic Medicine, IIGM, Turin, Italy; Department of Medical Sciences, University of Turin, Turin, Italy
| | - Clara Viberti
- Italian Institute for Genomic Medicine, IIGM, Turin, Italy; Department of Medical Sciences, University of Turin, Turin, Italy
| | - Giovanni Cugliari
- Italian Institute for Genomic Medicine, IIGM, Turin, Italy; Department of Medical Sciences, University of Turin, Turin, Italy
| | - Alessandra Allione
- Italian Institute for Genomic Medicine, IIGM, Turin, Italy; Department of Medical Sciences, University of Turin, Turin, Italy
| | - Elisabetta Casalone
- Italian Institute for Genomic Medicine, IIGM, Turin, Italy; Department of Medical Sciences, University of Turin, Turin, Italy
| | - Marta Betti
- Department of Health Sciences, University of Piemonte Orientale, Novara, Italy
| | - Daniela Ferrante
- Medical Statistics and Cancer Epidemiology Unit, Department of Translational Medicine, University of Piemonte Orientale, Novara, Italy; Cancer Epidemiology Unit, CPO-Piemonte, Novara, Italy
| | - Anna Aspesi
- Department of Health Sciences, University of Piemonte Orientale, Novara, Italy
| | | | - Federica Grosso
- Division of Medical Oncology, SS. Antonio e Biagio General Hospital, Alessandria, Italy
| | - Roberta Libener
- Pathology Unit, SS. Antonio e Biagio General Hospital, Alessandria, Italy
| | - Ezio Piccolini
- Pneumology Unit, Santo Spirito Hospital, Casale Monferrato (AL), Italy
| | - Dario Mirabelli
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy; Cancer Epidemiology Unit, CPO Piemonte, Turin, Italy; Interdepartmental Center for Studies on Asbestos and Other Toxic Particulates "G. Scansetti," University of Turin, Turin, Italy
| | - Irma Dianzani
- Department of Health Sciences, University of Piemonte Orientale, Novara, Italy; Interdepartmental Center for Studies on Asbestos and Other Toxic Particulates "G. Scansetti," University of Turin, Turin, Italy
| | - Corrado Magnani
- Medical Statistics and Cancer Epidemiology Unit, Department of Translational Medicine, University of Piemonte Orientale, Novara, Italy; Cancer Epidemiology Unit, CPO-Piemonte, Novara, Italy; Interdepartmental Center for Studies on Asbestos and Other Toxic Particulates "G. Scansetti," University of Turin, Turin, Italy
| | - Giuseppe Matullo
- Italian Institute for Genomic Medicine, IIGM, Turin, Italy; Department of Medical Sciences, University of Turin, Turin, Italy; Interdepartmental Center for Studies on Asbestos and Other Toxic Particulates "G. Scansetti," University of Turin, Turin, Italy; Medical Genetics Unit, AOU Città della Salute e della Scienza, Turin, Italy.
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25
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Otoukesh B, Boddouhi B, Moghtadaei M, Kaghazian P, Kaghazian M. Novel molecular insights and new therapeutic strategies in osteosarcoma. Cancer Cell Int 2018; 18:158. [PMID: 30349420 PMCID: PMC6192346 DOI: 10.1186/s12935-018-0654-4] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 10/01/2018] [Indexed: 12/18/2022] Open
Abstract
Osteosarcoma (OS) is one of the most prevalent malignant cancers with lower survival and poor overall prognosis mainly in children and adolescents. Identifying the molecular mechanisms and OS stem cells (OSCs) as new concepts involved in disease pathogenesis and progression may potentially lead to new therapeutic targets. Therefore, therapeutic targeting of OSCs can be one of the most important and effective strategies for the treatment of OS. This review describes the new molecular targets of OS as well as novel therapeutic approaches in the design of future investigations and treatment.
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Affiliation(s)
- Babak Otoukesh
- Bone and Joint Reconstruction Research Center, Shafa Orthopedic Hospital, Iran University of Medical Sciences, Tehran, 1445613131 Iran
| | - Bahram Boddouhi
- Bone and Joint Reconstruction Research Center, Shafa Orthopedic Hospital, Iran University of Medical Sciences, Tehran, 1445613131 Iran
| | - Mehdi Moghtadaei
- Bone and Joint Reconstruction Research Center, Shafa Orthopedic Hospital, Iran University of Medical Sciences, Tehran, 1445613131 Iran
| | - Peyman Kaghazian
- Department of Orthopedic and Traumatology, Universitätsklinikum Bonn, Bonn, Germany
| | - Maria Kaghazian
- Department of Biology, Jundishapur University of Medical Sciences, Ahvaz, Iran
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26
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Huang X, Wu C, Fu Y, Guo L, Kong X, Cai H. Methylation analysis for multiple gene promoters in non-small cell lung cancers in high indoor air pollution region in China. Bull Cancer 2018; 105:746-754. [PMID: 30126609 DOI: 10.1016/j.bulcan.2018.05.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 04/08/2018] [Accepted: 05/11/2018] [Indexed: 12/13/2022]
Abstract
AIM The prevalence and mortality rates of lung cancer in Xuanwei, Yunnan, China, are the highest in the world. The severe indoor air pollution caused by smoky coals with high benzo (a)pyrene (BaP) and quartz levels is the main environmental factor. The aim of this study was to investigate methylation profiles of promoters in eight genes in primary non-small cell lung cancers (NSCLC) exposed to smoky coals. MATERIALS AND METHODS Candidate genes including CDKN2A, DLEC1, CDH1, DAPK, RUNX3, APC, WIF1 and MGMT were determined for the promoter methylation status using Nested methylation-specific PCR (nMSP) in primary 23NSCLC tissues and in circulating tumor DNA (ctDNA) isolated from 42plasma samples (9matched to tissues) as well as 10healthy plasma samples, using Sanger sequencing to verify the results. RESULTS Seven of the 8genes, except MGMT, had relatively high methylation frequencies ranging from 39%-74% in tissues. Moreover, methylation frequencies in five genes identified in lung cancer plasma were 45% for CDKN2A, 48% for DLEC1, 76% for CDH1, 14% for DAPK, 29% for RUNX3, with a relatively good concordance of methylation among 9 tissues and paired plasma. However, the genes from all healthy plasma showed no methylation. CONCLUSIONS A panel of genes including CDKN2A, DLEC1, CDH1, DAPK and RUNX3 may be used as potential epigenetic biomarkers for early lung cancer detection. CDH1 promoter methylation was associated with lung cancer metastasis in areas of air pollution from buring of smoky coals. DLEC1 and CDH1 exhibited specific high methylation frequencies, different from previous reports.
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Affiliation(s)
- Xinwei Huang
- Kunming University of Science and Technology, Faculty of Environmental Science and Engineering, 650500 Kunming, Yunnan province, China; Kunming University of Science and Technology, Medical school, 650500 Kunming, Yunnan province, China; Kunming University of Science and Technology, Genetics and Pharmacogenomics Laboratory, 650500 Kunming, Yunnan province, China
| | - Chaoqun Wu
- Kunming University of Science and Technology, Medical school, 650500 Kunming, Yunnan province, China; Kunming University of Science and Technology, Genetics and Pharmacogenomics Laboratory, 650500 Kunming, Yunnan province, China
| | - Yu Fu
- Kunming University of Science and Technology, Medical school, 650500 Kunming, Yunnan province, China; Kunming University of Science and Technology, Genetics and Pharmacogenomics Laboratory, 650500 Kunming, Yunnan province, China
| | - Liqiong Guo
- Kunming University of Science and Technology, Medical school, 650500 Kunming, Yunnan province, China; Kunming University of Science and Technology, Genetics and Pharmacogenomics Laboratory, 650500 Kunming, Yunnan province, China
| | - Xiangyang Kong
- Kunming University of Science and Technology, Medical school, 650500 Kunming, Yunnan province, China; Kunming University of Science and Technology, Genetics and Pharmacogenomics Laboratory, 650500 Kunming, Yunnan province, China.
| | - Haibo Cai
- Yunfeng Hospital, Department of Oncology, 655400 Xuanwei City, Yunnan Province, China.
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Santarpia M, Liguori A, D'Aveni A, Karachaliou N, Gonzalez-Cao M, Daffinà MG, Lazzari C, Altavilla G, Rosell R. Liquid biopsy for lung cancer early detection. J Thorac Dis 2018; 10:S882-S897. [PMID: 29780635 DOI: 10.21037/jtd.2018.03.81] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Molecularly targeted therapies and immune checkpoint inhibitors have markedly improved the therapeutic management of advanced lung cancer. However, it still remains the leading cause of cancer-related mortality worldwide, with disease stage at diagnosis representing the main prognostic factor. Detection of lung cancer at an earlier stage of disease, potentially susceptible of curative resection, can be critical to improve patients survival. Low-dose computed tomography (LDCT) screening of high-risk patients has been demonstrated to reduce mortality from lung cancer, but can be also associated with high false-positive rate, thus often resulting in unnecessary interventions for patients. Novel sensitive and specific biomarkers for identification of high-risk subjects and early detection that can be used alternatively and/or complement current routine diagnostic procedures are needed. Liquid biopsy has recently demonstrated its clinical usefulness in advanced NSCLC as a surrogate of tissue biopsy for noninvasive assessment of specific genomic alterations, thereby providing prognostic and predictive information. Different biosources from liquid biopsy, including cell free circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), exosomes and tumor-educated platelets (TEPs), have also been widely investigated for their potential role in lung cancer diagnosis. This review will provide an overview on the circulating biomarkers being evaluated for lung cancer detection, mainly focusing on results from most recent studies, the techniques developed to perform their assessment in blood and other biologic fluids and challenges in their clinical applications.
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Affiliation(s)
- Mariacarmela Santarpia
- Medical Oncology Unit, Department of Human Pathology of Adult and Evolutive Age "G. Barresi", University of Messina, Messina, Italy
| | - Alessia Liguori
- Medical Oncology Unit, Department of Human Pathology of Adult and Evolutive Age "G. Barresi", University of Messina, Messina, Italy
| | - Alessandro D'Aveni
- Medical Oncology Unit, Department of Human Pathology of Adult and Evolutive Age "G. Barresi", University of Messina, Messina, Italy
| | - Niki Karachaliou
- Institute of Oncology Rosell (IOR), University Hospital Sagrat Cor, Barcelona, Spain
| | - Maria Gonzalez-Cao
- Department of Oncology, Institute of Oncology Rosell (IOR), Quirón-Dexeus University Institute, Barcelona, Spain
| | - Maria Grazia Daffinà
- Medical Oncology Unit, Department of Human Pathology of Adult and Evolutive Age "G. Barresi", University of Messina, Messina, Italy
| | - Chiara Lazzari
- Department of Oncology, Division of Experimental Medicine, IRCCS San Raffaele, Milan, Italy
| | - Giuseppe Altavilla
- Medical Oncology Unit, Department of Human Pathology of Adult and Evolutive Age "G. Barresi", University of Messina, Messina, Italy
| | - Rafael Rosell
- Cancer Biology and Precision Medicine Program, Germans Trias i Pujol University Hospital, Badalona, Spain.,Catalan Institute of Oncology, Germans Trias i Pujol University Hospital, Badalona, Spain
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28
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Gene methylation as a powerful biomarker for detection and screening of non-small cell lung cancer in blood. Oncotarget 2018; 8:31692-31704. [PMID: 28404957 PMCID: PMC5458240 DOI: 10.18632/oncotarget.15919] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 01/10/2017] [Indexed: 11/25/2022] Open
Abstract
DNA methylation has been reported to become a potential powerful tool for cancer detection and diagnosis. However, the possibilities for the application of blood-based gene methylation as a biomarker for non-small cell lung cancer (NSCLC) detection and screening remain unclear. Hence, we performed this meta-analysis to evaluate the value of gene methylation detected in blood samples as a noninvasive biomarker in NSCLC. A total of 28 genes were analyzed from 37 case-control studies. In the genes with more than three studies, we found that the methylation of P16, RASSF1A, APC, RARβ, DAPK, CDH13, and MGMT was significantly associated with risks of NSCLC. The methylation statuses of P16, RASSF1A, APC, RARβ, DAPK, CDH13, and MGMT were not linked to age, gender, smoking behavior, and tumor stage and histology in NSCLC. Therefore, the use of the methylation status of P16, RASSF1A, APC, RARβ, DAPK, CDH13, and MGMT could become a promising and powerful biomarker for the detection and screening of NSCLC in blood in clinical settings. Further large-scale studies with large sample sizes are necessary to confirm our findings in the future.
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Genome-wide DNA methylation profiles altered by Helicobacter pylori in gastric mucosa and blood leukocyte DNA. Oncotarget 2018; 7:37132-37144. [PMID: 27206798 PMCID: PMC5095064 DOI: 10.18632/oncotarget.9469] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/24/2016] [Indexed: 01/28/2023] Open
Abstract
Purpose To investigate Helicobacter pylori (H.pylori) associated genome-wide aberrant methylation patterns in gastric mucosa and blood leukocyte DNA, a population-based study was conducted in Linqu County. Results A total of 3000 and 386 CpGs were differentially methylated after successful H.pylori eradication in gastric mucosa and blood leukocyte DNA respectively, and 17 were the same alteration trend in the both tissues. The differentially methylated CpGs were located more frequently in promoters or CpG islands for gastric mucosa and gene body or open sea for blood leukocyte DNA. In eradicated gastric mucosa, the hypermethylated CpGs were enriched across inflammatory pathways, while the hypomethylated CpGs in tube morphogenesis, development and so on. The final validation found lower SPI1, PRIC285 and S1PR4 methylation levels in H.pylori positive subjects by case-control comparison, and increased methylation levels in H.pylori eradicated gastric mucosa by self-comparison. The Cancer Genome Atlas (TCGA) database analysis suggested that the up-regulation of the three genes by hypomethylation might be associated with gastric carcinogenesis. Experimental Design Infinium HumanMethylation 450K BeadChip was used to compare methylation profiles prior to and after eradication treatment. The methylation levels of identified candidate differentially methylated genes before and after H.pylori eradication were further validated by two stages (Stage I: self-comparison of 16 subjects before and after anti-H.pylori treatment; Stage II: case-control comparison of 25 H.pylori positive and 25 negative subjects and self-comparison of 50 anti-H.pylori treated subjects). Conclusions Novel H.pylori associated aberrant methylated genes were identified across the whole genome both in gastric mucosa and blood leukocyte DNA.
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Widschwendter M, Zikan M, Wahl B, Lempiäinen H, Paprotka T, Evans I, Jones A, Ghazali S, Reisel D, Eichner J, Rujan T, Yang Z, Teschendorff AE, Ryan A, Cibula D, Menon U, Wittenberger T. The potential of circulating tumor DNA methylation analysis for the early detection and management of ovarian cancer. Genome Med 2017; 9:116. [PMID: 29268796 PMCID: PMC5740748 DOI: 10.1186/s13073-017-0500-7] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/24/2017] [Indexed: 02/07/2023] Open
Abstract
Background Despite a myriad of attempts in the last three decades to diagnose ovarian cancer (OC) earlier, this clinical aim still remains a significant challenge. Aberrant methylation patterns of linked CpGs analyzed in DNA fragments shed by cancers into the bloodstream (i.e. cell-free DNA) can provide highly specific signals indicating cancer presence. Methods We analyzed 699 cancerous and non-cancerous tissues using a methylation array or reduced representation bisulfite sequencing to discover the most specific OC methylation patterns. A three-DNA-methylation-serum-marker panel was developed using targeted ultra-high coverage bisulfite sequencing in 151 women and validated in 250 women with various conditions, particularly in those associated with high CA125 levels (endometriosis and other benign pelvic masses), serial samples from 25 patients undergoing neoadjuvant chemotherapy, and a nested case control study of 172 UKCTOCS control arm participants which included serum samples up to two years before OC diagnosis. Results The cell-free DNA amount and average fragment size in the serum samples was up to ten times higher than average published values (based on samples that were immediately processed) due to leakage of DNA from white blood cells owing to delayed time to serum separation. Despite this, the marker panel discriminated high grade serous OC patients from healthy women or patients with a benign pelvic mass with specificity/sensitivity of 90.7% (95% confidence interval [CI] = 84.3–94.8%) and 41.4% (95% CI = 24.1–60.9%), respectively. Levels of all three markers plummeted after exposure to chemotherapy and correctly identified 78% and 86% responders and non-responders (Fisher’s exact test, p = 0.04), respectively, which was superior to a CA125 cut-off of 35 IU/mL (20% and 75%). 57.9% (95% CI 34.0–78.9%) of women who developed OC within two years of sample collection were identified with a specificity of 88.1% (95% CI = 77.3–94.3%). Sensitivity and specificity improved further when specifically analyzing CA125 negative samples only (63.6% and 87.5%, respectively). Conclusions Our data suggest that DNA methylation patterns in cell-free DNA have the potential to detect a proportion of OCs up to two years in advance of diagnosis and may potentially guide personalized treatment. The prospective use of novel collection vials, which stabilize blood cells and reduce background DNA contamination in serum/plasma samples, will facilitate clinical implementation of liquid biopsy analyses. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0500-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Martin Widschwendter
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK.
| | - Michal Zikan
- Gynaecologic Oncology Center, Department of Obstetrics & Gynaecology, First Faculty of Medicine & General University Hospital, Charles University, Prague, Czech Republic
| | - Benjamin Wahl
- GATC Biotech AG, Jakob-Stadler-Platz 7, 78467, Konstanz, Germany
| | | | - Tobias Paprotka
- GATC Biotech AG, Jakob-Stadler-Platz 7, 78467, Konstanz, Germany
| | - Iona Evans
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK
| | - Allison Jones
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK
| | - Shohreh Ghazali
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK
| | - Daniel Reisel
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK
| | | | - Tamas Rujan
- Genedata AG, Margarethenstrasse 38, 4053, Basel, Switzerland
| | - Zhen Yang
- CAS Max-Planck Partner Institute for Computational Biology, Shanghai Institute of Biological Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Andrew E Teschendorff
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK.,CAS Max-Planck Partner Institute for Computational Biology, Shanghai Institute of Biological Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Andy Ryan
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK
| | - David Cibula
- Gynaecologic Oncology Center, Department of Obstetrics & Gynaecology, First Faculty of Medicine & General University Hospital, Charles University, Prague, Czech Republic
| | - Usha Menon
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK
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Diagnostic accuracy of DNA methylation in detection of gastric cancer: a meta-analysis. Oncotarget 2017; 8:113142-113152. [PMID: 29348893 PMCID: PMC5762578 DOI: 10.18632/oncotarget.22613] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 10/04/2017] [Indexed: 12/19/2022] Open
Abstract
Emerging studies demonstrate the diagnostic utility of DNA methylation-based blood test for gastric cancer. The aim of the meta-analysis is to evaluate the accuracy of blood DNA methylation markers for detecting patients with gastric cancer. A systematic literature search to November 2016 that evaluated DNA methylation markers utilizing blood specimen to detect gastric cancer were selected to derive pooled sensitivities and specificities. 32 studies including 4,172 patients (gastric cancer (N = 2,098), control (N = 2,074)) met the study criteria. Overall sensitivity of DNA methylation-based blood test for detecting gastric cancer was 57% (95% CI 50–63%); specificity was 97% (95% CI 95–98%). Among patients who received plasma-based testing, sensitivity was 71% (95% CI 59–81%); specificity was 89% (95% CI 78–94%). Among patients who received serum-based testing, sensitivity was 50% (95% CI 43–58%); specificity was 98% (95% CI 96–99%). Using multiple methylated genes had sensitivity of 76% (95% CI 64–84%); specificity of 85% (95% CI 65–95%). DNA methylation test had sensitivity of 55% (95% CI 47–64%) and specificity of 96% (95% CI 92–98%) for detecting TNM stage I+II gastric cancer. In conclusion, blood-based DNA methylation test had high specificity but modest sensitivity for detecting gastric cancer. Evaluating multiple methylated genes or using plasma sample may improve the diagnostic sensitivity.
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32
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Tang Y, Qiao G, Xu E, Xuan Y, Liao M, Yin G. Biomarkers for early diagnosis, prognosis, prediction, and recurrence monitoring of non-small cell lung cancer. Onco Targets Ther 2017; 10:4527-4534. [PMID: 28979144 PMCID: PMC5602468 DOI: 10.2147/ott.s142149] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Despite advances in the management of non-small cell lung cancer, it remains to be the leading cause of cancer-related deaths worldwide primarily because of diagnosis at a late stage with an overall 5-year survival rate of 17%. A reduction in mortality was achieved by low-dose computed tomography screening of high-risk patients. However, the benefit was later challenged by the high false positive rate, resulting in unnecessary follow-ups, thus entailing a burden on both the health care system and the individual. The diagnostic dilemma imposed by imaging modalities has created a need for the development of biomarkers capable of differentiating benign nodules from malignant ones. In the past decade, with the advancements in high-throughput profiling technologies, a huge amount of work has been done to derive biomarkers to supplement clinical diagnosis. However, only a few of them have efficient sensitivity and specificity to be utilized in clinical settings. Therefore, there is an urgent need for the development of sensitive and specific means to detect and diagnose lung cancers at an early stage, when curative interventions are still possible. Due to the invasiveness of tissue biopsies and inability to capture tumor heterogeneity, nowadays enormous efforts have been invested in the development of technologies and biomarkers that enable sensitive and cost-effective testing using substrates that can be obtained in a noninvasive manner. This review, primarily focusing on liquid biopsy, summarizes all documented potential biomarkers for diagnosis, monitoring recurrence treatment response.
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Affiliation(s)
- Yong Tang
- Southern Medical University, Guangzhou, Guangdong Province, China.,Department of Thoracic Surgery, General Hospital of Guangzhou Military Command of PLA, Yuexiu District, Guangzhou City, Guangdong Province, China
| | - Guibin Qiao
- Southern Medical University, Guangzhou, Guangdong Province, China.,Department of Thoracic Surgery, General Hospital of Guangzhou Military Command of PLA, Yuexiu District, Guangzhou City, Guangdong Province, China
| | - Enwu Xu
- Department of Thoracic Surgery, General Hospital of Guangzhou Military Command of PLA, Yuexiu District, Guangzhou City, Guangdong Province, China
| | - Yiwen Xuan
- Department of Thoracic Surgery, General Hospital of Guangzhou Military Command of PLA, Yuexiu District, Guangzhou City, Guangdong Province, China
| | - Ming Liao
- Department of Thoracic Surgery, General Hospital of Guangzhou Military Command of PLA, Yuexiu District, Guangzhou City, Guangdong Province, China
| | - Guilin Yin
- Southern Medical University, Guangzhou, Guangdong Province, China
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Xiang S, Xiang T, Xiao Q, Li Y, Shao B, Luo T. Zinc-finger protein 545 is inactivated due to promoter methylation and functions as a tumor suppressor through the Wnt/β-catenin, PI3K/AKT and MAPK/ERK signaling pathways in colorectal cancer. Int J Oncol 2017; 51:801-811. [PMID: 28677721 PMCID: PMC5564408 DOI: 10.3892/ijo.2017.4064] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 06/26/2017] [Indexed: 12/31/2022] Open
Abstract
The transcription factor, zinc-finger protein 545 (ZNF545), that belongs to the Kruppel-associated box zinc-finger protein (KRAB-ZFP) family, acts as a tumor suppressor and is inactivated by promoter methylation in cancers such as nasopharyngeal carcinoma, breast cancer, and gastric cancer, but its role in colorectal cancer (CRC) is unknown. The purpose of this study was to characterize the ZNF545 expression, methylation status, biological function, and related molecular mechanisms in CRC. The results showed that ZNF545 was expressed in adult normal colorectal tissues, but downregulated or silenced in CRC cell lines, and this mechanism was reversed by demethylation treatment with 5-aza-2′-deoxycytidine and trichostatin A. The results also showed that the expression of ZNF545 in primary CRC tissues was significantly downregulated compared to adjacent tissues (p<0.05). Overexpression of ZNF545 caused CRC cell cycle arrest and apoptosis, suppressed cell proliferation, and suppressed colony formation and migration in vitro, showing that ZNF545 can function as a tumor suppressor. This function was also shown in nude mice. Furthermore, Wnt/β-catenin, phosphatidylinositol 3 kinase/protein kinase B (PI3K/AKT), and mitogen-activated protein kinases/extracellular signal-regulated kinase (MAPK/ERK) signaling pathways participated in the regulation of ZNF545 in CRC cells. Together, the results suggested that ZNF545 functions as a tumor suppressor in CRC and is frequently inactivated by promoter methylation.
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Affiliation(s)
- Shili Xiang
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Tingxiu Xiang
- Molecular Oncology and Epigenetics Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Qian Xiao
- Department of Breast and Thyroid, The Hospital of Chongqing Traditional Chinese Medicine, Chongqing 400011, P.R. China
| | - Yunhai Li
- Molecular Oncology and Epigenetics Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Bianfei Shao
- Molecular Oncology and Epigenetics Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Tao Luo
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
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Kirby MK, Ramaker RC, Roberts BS, Lasseigne BN, Gunther DS, Burwell TC, Davis NS, Gulzar ZG, Absher DM, Cooper SJ, Brooks JD, Myers RM. Genome-wide DNA methylation measurements in prostate tissues uncovers novel prostate cancer diagnostic biomarkers and transcription factor binding patterns. BMC Cancer 2017; 17:273. [PMID: 28412973 PMCID: PMC5392915 DOI: 10.1186/s12885-017-3252-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 04/01/2017] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Current diagnostic tools for prostate cancer lack specificity and sensitivity for detecting very early lesions. DNA methylation is a stable genomic modification that is detectable in peripheral patient fluids such as urine and blood plasma that could serve as a non-invasive diagnostic biomarker for prostate cancer. METHODS We measured genome-wide DNA methylation patterns in 73 clinically annotated fresh-frozen prostate cancers and 63 benign-adjacent prostate tissues using the Illumina Infinium HumanMethylation450 BeadChip array. We overlaid the most significantly differentially methylated sites in the genome with transcription factor binding sites measured by the Encyclopedia of DNA Elements consortium. We used logistic regression and receiver operating characteristic curves to assess the performance of candidate diagnostic models. RESULTS We identified methylation patterns that have a high predictive power for distinguishing malignant prostate tissue from benign-adjacent prostate tissue, and these methylation signatures were validated using data from The Cancer Genome Atlas Project. Furthermore, by overlaying ENCODE transcription factor binding data, we observed an enrichment of enhancer of zeste homolog 2 binding in gene regulatory regions with higher DNA methylation in malignant prostate tissues. CONCLUSIONS DNA methylation patterns are greatly altered in prostate cancer tissue in comparison to benign-adjacent tissue. We have discovered patterns of DNA methylation marks that can distinguish prostate cancers with high specificity and sensitivity in multiple patient tissue cohorts, and we have identified transcription factors binding in these differentially methylated regions that may play important roles in prostate cancer development.
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Affiliation(s)
- Marie K. Kirby
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
- Present Address: TRM Oncology, 5901-C Peachtree Dunwoody Rd, Suite 200, Atlanta, GA 30328 USA
| | - Ryne C. Ramaker
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
- Department of Genetics, Kaul Human Genetics Building, Suite 230, 720 20th Street South, Birmingham, AL 35294 USA
| | - Brian S. Roberts
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
| | | | - David S. Gunther
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
- Present Address: University of Southern California, University Park, Los Angeles, CA 90089 USA
| | - Todd C. Burwell
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
- Present Address: Boeing Co., 499 Boeing Blvd, SW, Huntsville, AL 35824 USA
| | - Nicholas S. Davis
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
- Present Address: Duke University, 101 Science Drive, Durham, NC 27708 USA
| | - Zulfiqar G. Gulzar
- Department of Urology, Stanford University Medical Center, Room S287, 300 Pasteur Drive, Stanford, CA 94305-5118 USA
- Present Address: NuGEN technologies, 201 Industrial Rd #310, San Carlos, CA 94070 USA
| | - Devin M. Absher
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
| | - Sara J. Cooper
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
| | - James D. Brooks
- Department of Urology, Stanford University Medical Center, Room S287, 300 Pasteur Drive, Stanford, CA 94305-5118 USA
| | - Richard M. Myers
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
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Han X, Wang J, Sun Y. Circulating Tumor DNA as Biomarkers for Cancer Detection. GENOMICS, PROTEOMICS & BIOINFORMATICS 2017; 15:59-72. [PMID: 28392479 PMCID: PMC5414889 DOI: 10.1016/j.gpb.2016.12.004] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 12/13/2016] [Accepted: 12/20/2016] [Indexed: 12/23/2022]
Abstract
Detection of circulating tumor DNAs (ctDNAs) in cancer patients is an important component of cancer precision medicine ctDNAs. Compared to the traditional physical and biochemical methods, blood-based ctDNA detection offers a non-invasive and easily accessible way for cancer diagnosis, prognostic determination, and guidance for treatment. While studies on this topic are currently underway, clinical translation of ctDNA detection in various types of cancers has been attracting much attention, due to the great potential of ctDNA as blood-based biomarkers for early diagnosis and treatment of cancers. ctDNAs are detected and tracked primarily based on tumor-related genetic and epigenetic alterations. In this article, we reviewed the available studies on ctDNA detection and described the representative methods. We also discussed the current understanding of ctDNAs in cancer patients and their availability as potential biomarkers for clinical purposes. Considering the progress made and challenges involved in accurate detection of specific cell-free nucleic acids, ctDNAs hold promise to serve as biomarkers for cancer patients, and further validation is needed prior to their broad clinical use.
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Affiliation(s)
- Xiao Han
- CAS Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junyun Wang
- CAS Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yingli Sun
- CAS Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
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Zhong X, Shen H, Mao J, Zhang J, Han W. Epigenetic silencing of protocadherin 10 in colorectal cancer. Oncol Lett 2017; 13:2449-2453. [PMID: 28454418 PMCID: PMC5403191 DOI: 10.3892/ol.2017.5733] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 12/20/2016] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common types of malignant tumor in the world and occurs through a multi-step process resulting from the accumulation of genetic and epigenetic alterations of the genome. Although the molecular mechanisms of the pathogenesis of CRC remain unclear, the inactivation of tumor suppressor genes (TSGs) through promoter methylation serves an important role. Aberrant methylation is a well-defined marker of CRC. At present, the epigenetic silencing of protocadherin 10 (PCDH10) has been identified as an important TSG with key roles in colorectal carcinogenesis, invasion and metastasis as a frequent and early event. Advances in gene methylation detection in tumor tissues and body fluids have led to the development of non-invasive screening methods for CRC. The present study aimed to review the epigenetic alteration of PCDH10 in CRC development, and the potential of PCDH10 to be a non-invasive biomarker for CRC.
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Affiliation(s)
- Xian Zhong
- Department of Medical Oncology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
- Department of Medical Oncology, Hangzhou Binjiang Hospital, Hangzhou, Zhejiang 310052, P.R. China
| | - Hong Shen
- Department of Medical Oncology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Jianshan Mao
- Department of Gastroenterology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Jiawei Zhang
- Cancer Institute, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Weidong Han
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, P.R. China
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37
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Liu Y. The context of prostate cancer genomics in personalized medicine. Oncol Lett 2017; 13:3347-3353. [PMID: 28521441 DOI: 10.3892/ol.2017.5911] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 01/26/2017] [Indexed: 12/31/2022] Open
Abstract
Prostate cancer is one of the most common types of cancer in males. Heterogeneous genomic aberrations may lead to prostate cancer onset, progression and metastasis. This heterogeneity also contributes to the variety in cancer risk and outcomes, different drug responses and progression, observed between individual patients. Classical prognostic factors, including prostate-specific antigen, Gleason Score and clinical tumor staging, are not sufficient to portray the complexity of a clinically relevant cancer diagnosis, risk prognosis, treatment choice and therapy monitoring. There is a requirement for novel genetic biomarkers in order to understand the oncogenic heterogeneity in a patient-personalized clinical setting and to improve the efficacy of risk prognosis and treatment choice. A number of biomarkers and gene panels have been established from patient sample cohort studies. These previous studies have provided distinct information to the investigation of heterogeneous malignancy in prostate cancer, which aids in clinical decision-making. Biomarker-guided therapies may facilitate the effective selection of drugs during early treatment; therefore, are beneficial to the individual patient. A non-invasive approach allows for convenient and repeated sampling to screen for cancer and monitor treatment response without the requirement for invasive tissue biopsies. With the current availability of numerous advanced technologies, reliable detection of the minimal tumor residues present following treatment may become clinical practice and, therefore, inform further in the field of personalized medicine.
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Affiliation(s)
- Yanling Liu
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm SE-171 76, Sweden
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38
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Wang J, Han X, Sun Y. DNA methylation signatures in circulating cell-free DNA as biomarkers for the early detection of cancer. SCIENCE CHINA-LIFE SCIENCES 2017; 60:356-362. [DOI: 10.1007/s11427-016-0253-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 11/16/2016] [Indexed: 02/06/2023]
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Altobelli E, Angeletti PM, Latella G. Role of Urinary Biomarkers in the Diagnosis of Adenoma and Colorectal Cancer: A Systematic Review and Meta-Analysis. J Cancer 2016; 7:1984-2004. [PMID: 27877214 PMCID: PMC5118662 DOI: 10.7150/jca.16244] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 07/16/2016] [Indexed: 12/23/2022] Open
Abstract
The growing interest in enhancing and spreading colorectal cancer (CRC) screening has been stimulating the exploration of novel biomarkers with greater sensitivity and specificity than immunochemical faecal occult blood test (iFOBT). The present study provides i) a systematic review of the urinary biomarkers that have been tested to achieve early CRC diagnosis and assess the risk of colorectal adenoma and adenocarcinoma, and ii) a meta-analysis of the data regarding the urinary prostaglandin (PG) metabolite PGE-M. As regard to gene markers, we found significantly different percent methylation of the vimentin gene in CRC patients and healthy controls (HC) (p<0.0001). Respect to metabolism of nitrogenous bases, cytidine, 1-methyladenosine, and adenosine, have higher concentrations in CRC patients than in HC (respectively, p<0.01, p=0.01, and p<0.01). As regard to spermine we found that N1,N12 diacetyl spermine (DiAcSpm) and N1, N8 diacetylspermidine (DiAcSpd) were significantly higher in CRC than in HC (respectively p=0.01 and p<0.01). Respect to PGE-M, levels were higher in CRC than in those with multiple polyposis (p<0.006) and HC subjects (p<0.0004). PGE-M seems to be the most interesting and promising urinary marker for CRC and adenoma risk assessment and for CRC screening. In conclusion, evidence suggests that urinary biomarker could have a potential role as urinary biomarkers in the diagnosis of colorectal cancer. Particularly, PGE-M seems to be the most promising urinary marker for CRC early detection.
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Affiliation(s)
- Emma Altobelli
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
- Epidemiology and Biostatistics Unit, AUSL Teramo, University of L'Aquila, L'Aquila, Italy
| | - Paolo Matteo Angeletti
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Giovanni Latella
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
- Gastroenterology Unit, Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
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Chen F, Huang T, Ren Y, Wei J, Lou Z, Wang X, Fan X, Chen Y, Weng G, Yao X. Clinical significance of CDH13 promoter methylation as a biomarker for bladder cancer: a meta-analysis. BMC Urol 2016; 16:52. [PMID: 27578166 PMCID: PMC5004266 DOI: 10.1186/s12894-016-0171-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/23/2016] [Indexed: 12/21/2022] Open
Abstract
Background Methylation of the tumor suppressor gene H-cadherin (CDH13) has been reported in many cancers. However, the clinical effect of the CDH13 methylation status of patients with bladder cancer remains to be clarified. Methods A systematic literature search was performed to identify eligible studies in the PubMed, Embase, EBSCO, CKNI and Wanfang databases. The pooled odds ratio (OR) and the corresponding 95 % confidence interval (95 % CI) was calculated and summarized. Results Nine eligible studies were included in the present meta-analysis consisting of a total of 1017 bladder cancer patients and 265 non-tumor controls. A significant association was found between CDH13 methylation levels and bladder cancer (OR = 21.71, P < 0.001). The results of subgroup analyses based on sample type suggested that CDH13 methylation was significantly associated with bladder cancer risk in both the tissue and the urine (OR = 53.94, P < 0.001; OR = 7.71, P < 0.001; respectively). A subgroup analysis based on ethnic population showed that the OR value of methylated CDH13 was higher in Asians than in Caucasians (OR = 35.18, P < 0.001; OR = 8.86, P < 0.001; respectively). The relationships between CDH13 methylation and clinicopathological features were also analyzed. A significant association was not observed between CDH13 methylation status and gender (P = 0.053). Our results revealed that CDH13 methylation was significantly associated with high-grade bladder cancer, multiple bladder cancer and muscle invasive bladder cancer (OR = 2.22, P < 0.001; OR = 1.45, P = 0.032; OR = 3.42, P < 0.001; respectively). Conclusion Our study indicates that CDH13 methylation may play an important role in the carcinogenesis, development and progression of bladder cancer. In addition, CDH13 methylation has the potential to be a useful biomarker for bladder cancer screening in urine samples and to be a prognostic biomarker in the clinic. Electronic supplementary material The online version of this article (doi:10.1186/s12894-016-0171-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Feng Chen
- Laboratory of Kidney Carcinoma, Ningbo urology & Nephrology Hospital, Ningbo, 315040, Zhejiang, China
| | - Tao Huang
- Laboratory of Kidney Carcinoma, Ningbo urology & Nephrology Hospital, Ningbo, 315040, Zhejiang, China
| | - Yu Ren
- Laboratory of Kidney Carcinoma, Ningbo urology & Nephrology Hospital, Ningbo, 315040, Zhejiang, China
| | - Junjun Wei
- Laboratory of Kidney Carcinoma, Ningbo urology & Nephrology Hospital, Ningbo, 315040, Zhejiang, China
| | - Zhongguan Lou
- Laboratory of Kidney Carcinoma, Ningbo urology & Nephrology Hospital, Ningbo, 315040, Zhejiang, China
| | - Xue Wang
- Laboratory of Kidney Carcinoma, Ningbo urology & Nephrology Hospital, Ningbo, 315040, Zhejiang, China
| | - Xiaoxiao Fan
- Laboratory of Kidney Carcinoma, Ningbo urology & Nephrology Hospital, Ningbo, 315040, Zhejiang, China
| | - Yirun Chen
- Laboratory of Kidney Carcinoma, Ningbo urology & Nephrology Hospital, Ningbo, 315040, Zhejiang, China
| | - Guobin Weng
- Laboratory of Kidney Carcinoma, Ningbo urology & Nephrology Hospital, Ningbo, 315040, Zhejiang, China
| | - Xuping Yao
- Laboratory of Kidney Carcinoma, Ningbo urology & Nephrology Hospital, Ningbo, 315040, Zhejiang, China.
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Weiss G, Schlegel A, Kottwitz D, König T, Tetzner R. Validation of the SHOX2/PTGER4 DNA Methylation Marker Panel for Plasma-Based Discrimination between Patients with Malignant and Nonmalignant Lung Disease. J Thorac Oncol 2016; 12:77-84. [PMID: 27544059 PMCID: PMC5226366 DOI: 10.1016/j.jtho.2016.08.123] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/15/2016] [Accepted: 08/09/2016] [Indexed: 12/17/2022]
Abstract
Introduction Low-dose computed tomography (LDCT) is used for screening for lung cancer (LC) in high-risk patients in the United States. The definition of high risk and the impact of frequent false-positive results of low-dose computed tomography remains a challenge. DNA methylation biomarkers are valuable noninvasive diagnostic tools for cancer detection. This study reports on the evaluation of methylation markers in plasma DNA for LC detection and discrimination of malignant from nonmalignant lung disease. Methods Circulating DNA was extracted from 3.5-mL plasma samples, treated with bisulfite using a commercially available kit, purified, and assayed by real-time polymerase chain reaction for assessment of DNA methylation of short stature homeobox 2 gene (SHOX2), prostaglandin E receptor 4 gene (PTGER4), and forkhead box L2 gene (FOXL2). In three independent case-control studies these assays were evaluated and optimized. The resultant assay, a triplex polymerase chain reaction combining SHOX2, PTGER4, and the reference gene actin, beta gene (ACTB), was validated using plasma from patients with and without malignant disease. Results A panel of SHOX2 and PTGER4 provided promising results in three independent case-control studies examining a total of 330 plasma specimens (area under the receiver operating characteristic curve = 91%–98%). A validation study with 172 patient samples demonstrated significant discriminatory performance in distinguishing patients with LC from subjects without malignancy (area under the curve = 0.88). At a fixed specificity of 90%, sensitivity for LC was 67%; at a fixed sensitivity of 90%, specificity was 73%. Conclusions Measurement of SHOX2 and PTGER4 methylation in plasma DNA allowed detection of LC and differentiation of nonmalignant diseases. Development of a diagnostic test based on this panel may provide clinical utility in combination with current imaging techniques to improve LC risk stratification.
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Huang C, Zhou X, Li Z, Liu H, He Y, Ye G, Huang K. Downregulation of thrombospondin-1 by DNA hypermethylation is associated with tumor progression in laryngeal squamous cell carcinoma. Mol Med Rep 2016; 14:2489-96. [PMID: 27485791 PMCID: PMC4991671 DOI: 10.3892/mmr.2016.5580] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Accepted: 07/25/2016] [Indexed: 11/05/2022] Open
Abstract
Thrombospondin-1 (THBS-1) has been demonstrated to have a complicated role in human cancer and to exert stimulatory and inhibitory effects in different types of tumors. DNA methylation, as the most frequent mechanism for gene silencing, has been widely investigated in regards to the development of tumors. However, the expression levels and methylation status of THBS-1, and their roles in laryngeal squamous cell carcinoma (LSCC) remain to be elucidated. The present study detected downregulated THBS-1 mRNA and protein expression levels in LSCC by using reverse transcription-quantitative polymerase chain reaction (PCR) and western blotting, while decreased expression levels of THBS-1 mRNA and protein were significantly associated with lymph node metastasis and tumor-node-metastasis (TNM) stage. Furthermore, aberrant methylation of THBS-1 was frequently observed in LSCC by methylation-specific PCR, particularly in tumor tissues from lymph node metastasis or samples from cancer with advanced TNM stage. Furthermore, the current study demonstrated that downregulated expression of THBS-1 in LSCC was consistent with aberrant methylation of this gene. Treatment with the DNA methyltransferase inhibitor 5-aza-2′-deoxy-cytidine in Hep-2 cells induced demethylation of THBS-1, enhanced THBS-1 expression, and inhibited the proliferative and invasive ability of Hep-2 cells. Collectively, the results of the present study suggest that THBS-1 may exert an inhibitory effect in the development of LSCC. Aberrant methylation was an important reason for the downregulation of THBS-1 and was involved in the invasion and metastasis of LSCC. Demethylating agents may be effective candidates for the treatment of LSCC.
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Affiliation(s)
- Chuang Huang
- Department of Head and Neck Surgery, Chongqing Cancer Institute, Chongqing 400030, P.R. China
| | - Xiaohong Zhou
- Department of Head and Neck Surgery, Chongqing Cancer Institute, Chongqing 400030, P.R. China
| | - Zhenhua Li
- Department of Head and Neck Surgery, Chongqing Cancer Institute, Chongqing 400030, P.R. China
| | - Hong Liu
- Department of Head and Neck Surgery, Chongqing Cancer Institute, Chongqing 400030, P.R. China
| | - Yun He
- Department of Head and Neck Surgery, Chongqing Cancer Institute, Chongqing 400030, P.R. China
| | - Guo Ye
- Department of Head and Neck Surgery, Chongqing Cancer Institute, Chongqing 400030, P.R. China
| | - Kun Huang
- Department of Dermatology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
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Matthaios D, Balgkouranidou I, Karayiannakis A, Bolanaki H, Xenidis N, Amarantidis K, Chelis L, Romanidis K, Chatzaki A, Lianidou E, Trypsianis G, Kakolyris S. Methylation status of the APC and RASSF1A promoter in cell-free circulating DNA and its prognostic role in patients with colorectal cancer. Oncol Lett 2016; 12:748-756. [PMID: 27347211 DOI: 10.3892/ol.2016.4649] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 04/29/2016] [Indexed: 01/26/2023] Open
Abstract
DNA methylation is the most frequent epigenetic alteration. Using methylation-specific polymerase chain reaction (MSP), the methylation status of the adenomatous polyposis coli (APC) and Ras association domain family 1 isoform A (RASSF1A) genes was examined in cell-free circulating DNA from 155 plasma samples obtained from patients with early and advanced colorectal cancer (CRC). APC and RASSF1A hypermethylation was frequently observed in both early and advanced disease, and was significantly associated with a poorer disease outcome. The methylation status of the APC and RASSF1A promoters was investigated in cell-free DNA of patients with CRC. Using MSP, the promoter methylation status of APC and RASSF1A was examined in 155 blood samples obtained from patients with CRC, 88 of whom had operable CRC (oCRC) and 67 had metastatic CRC (mCRC). The frequency of APC methylation in patients with oCRC was 33%. Methylated APC promoter was significantly associated with older age (P=0.012), higher stage (P=0.014) and methylated RASSF1A status (P=0.050). The frequency of APC methylation in patients with mCRC was 53.7%. In these patients, APC methylation was significantly associated with methylated RASSF1A status (P=0.016). The frequency of RASSF1A methylation in patients with oCRC was 25%. Methylated RASSF1A in oCRC was significantly associated with higher stage (P=0.021). The frequency of RASSF1A methylation in mCRC was 44.8%. Methylated RASSF1A in mCRC was associated with moderate differentiation (P=0.012), high levels of carcinoembryonic antigen (P=0.023) and methylated APC status (P=0.016). Patients with an unmethylated APC gene had better survival in both early (81±5 vs. 27±4 months, P<0.001) and advanced disease (37±7 vs. 15±3 months, P<0.001), compared with patients with methylated APC. Patients with an unmethylated RASSF1A gene had better survival in both early (71±6 vs. 46±8 months, P<0.001) and advanced disease (28±4 vs. 16±3 months, P<0.001) than patients with methylated RASSF1A. The observed significant correlations between APC and RASSF1A promoter methylation status and survival may be indicative of a prognostic role for these genes in CRC, which requires additional testing in larger studies.
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Affiliation(s)
- Dimitrios Matthaios
- Department of Medical Oncology, Medical School, Democritus University of Thrace, University General Hospital of Alexandroupolis, Alexandroupolis 68100, Greece
| | - Ioanna Balgkouranidou
- Department of Medical Oncology, Medical School, Democritus University of Thrace, University General Hospital of Alexandroupolis, Alexandroupolis 68100, Greece
| | - Anastasios Karayiannakis
- Second Department of Surgery, Medical School, Democritus University of Thrace, University General Hospital of Alexandroupolis, Alexandroupolis 68100, Greece
| | - Helen Bolanaki
- Second Department of Surgery, Medical School, Democritus University of Thrace, University General Hospital of Alexandroupolis, Alexandroupolis 68100, Greece
| | - Nikolaos Xenidis
- Department of Medical Oncology, Medical School, Democritus University of Thrace, University General Hospital of Alexandroupolis, Alexandroupolis 68100, Greece
| | - Kyriakos Amarantidis
- Department of Medical Oncology, Medical School, Democritus University of Thrace, University General Hospital of Alexandroupolis, Alexandroupolis 68100, Greece
| | - Leonidas Chelis
- Department of Medical Oncology, Medical School, Democritus University of Thrace, University General Hospital of Alexandroupolis, Alexandroupolis 68100, Greece
| | - Konstantinos Romanidis
- Second Department of Surgery, Medical School, Democritus University of Thrace, University General Hospital of Alexandroupolis, Alexandroupolis 68100, Greece
| | - Aikaterini Chatzaki
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, University General Hospital of Alexandroupolis, Alexandroupolis 68100, Greece
| | - Evi Lianidou
- Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, Athens 15771, Greece
| | - Grigorios Trypsianis
- Laboratory of Statistics, Medical School, Democritus University of Thrace, University General Hospital of Alexandroupolis, Alexandroupolis 68100, Greece
| | - Stylianos Kakolyris
- Department of Medical Oncology, Medical School, Democritus University of Thrace, University General Hospital of Alexandroupolis, Alexandroupolis 68100, Greece
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44
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Manoochehri M, Borhani N, Karbasi A, Koochaki A, Kazemi B. Promoter hypermethylation and downregulation of the FAS gene may be involved in colorectal carcinogenesis. Oncol Lett 2016; 12:285-290. [PMID: 27347139 DOI: 10.3892/ol.2016.4578] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 04/01/2016] [Indexed: 12/23/2022] Open
Abstract
Aberrant DNA methylation has been investigated in carcinogenesis and as biomarker for the early detection of colorectal cancer (CRC). The present study aimed to define the methylation status in the regulatory elements of two proapoptotic genes, Fas cell surface death receptor (FAS) and BCL2-associated X protein (BAX). DNA methylation analysis was performed in tumor and adjacent normal tissue using HpaII/MspI restriction digestion and methylation-specific polymerase chain reaction (PCR). The results observed downregulation of the FAS and BAX genes in the CRC tissues compared with the adjacent normal samples. Furthermore, demethylation using 5-aza-2'-deoxycytidine treatment followed by reverse-transcription quantitative PCR were performed on the HT-29 cell line to measure BAX and FAS mRNA expression following demethylation. The 5-aza-2'-deoxycytidine treatment resulted in significant FAS gene upregulation in the HT-29 cell line, but no significant difference in BAX expression. Furthermore, analysis of CpG islands in the FAS gene promoter revealed that the FAS promoter was significantly hypermethylated in 53.3% of tumor tissues compared with adjacent normal samples. Taken together, the results indicate that decreased expression of the FAS gene due to hypermethylation of its promoter may lead to apoptotic resistance, and acts as an important step during colorectal carcinogenesis.
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Affiliation(s)
- Mehdi Manoochehri
- Biotechnology Department, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran 19857-17453, Iran; School of Medicine, Shahroud University of Medical Sciences, Shahroud 36247-73955, Iran
| | - Nasim Borhani
- School of Medicine, Shahroud University of Medical Sciences, Shahroud 36247-73955, Iran
| | - Ashraf Karbasi
- Gastroenterology and Hepatology Department, Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran 14359-15371, Iran
| | - Ameneh Koochaki
- Cell and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran 19857-17453, Iran
| | - Bahram Kazemi
- Biotechnology Department, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran 19857-17453, Iran; Cell and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran 19857-17453, Iran
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45
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Deng QK, Lei YG, Lin YL, Ma JG, Li WP. Prognostic Value of Protocadherin10 (PCDH10) Methylation in Serum of Prostate Cancer Patients. Med Sci Monit 2016; 22:516-21. [PMID: 26881880 PMCID: PMC4758335 DOI: 10.12659/msm.897179] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Background Prostate cancer is a heterogeneous malignancy with outcome difficult to predict. Currently, there is an urgent need to identify novel biomarkers that can accurately predict patient outcome and improve the treatment strategy. The aim of this study was to investigate the methylation status of PCDH10 in serum of prostate cancer patients and its potential relevance to clinicopathological features and prognosis. Material/Methods The methylation status of PCDH10 in serum of 171 primary prostate cancer patients and 65 controls was evaluated by methylation-specific PCR (MSP), after which the relationship between PCDH10 methylation and clinicopathologic features was evaluated. Kaplan-Meier survival analysis and Cox analysis were used to evaluate the correlation between PCDH10 methylation and prognosis. Results PCDH10 methylation occurred frequently in serum of prostate cancer patients. Moreover, PCDH10 methylation was significantly associated with higher preoperative PSA level, advanced clinical stage, higher Gleason score, lymph node metastasis, and biochemical recurrence (BCR). In addition, patients with methylated PCDH10 had shorter BCR-free survival and overall survival than patients with unmethylated PCDH10. Univariate and multivariate Cox proportional hazards model analysis indicated that PCDH10 methylation in serum is an independent predictor of worse BCR-free survival and overall survival. Conclusions PCDH10 methylation in serum is a potential prognostic biomarker for prostate cancer.
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Affiliation(s)
- Qiu-Kui Deng
- Department of Orthopaedics, Qilu Hospital, Shandong University, Jinan, Shandong, China (mainland)
| | - Yong-Gang Lei
- Department of Urology, Weinan Central Hospital, Weinan, Shaanxi, China (mainland)
| | - Ying-Li Lin
- Department of Urology, Xuzhou Cancer Hospital, Affiliated Xuzhou Hospital of Jiangsu University, Xuzhou, Jiangsu, China (mainland)
| | - Jian-Guo Ma
- Department of Urology, Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, China (mainland)
| | - Wen-Ping Li
- Department of Urology, Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, China (mainland)
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46
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Robust Detection of DNA Hypermethylation of ZNF154 as a Pan-Cancer Locus with in Silico Modeling for Blood-Based Diagnostic Development. J Mol Diagn 2016; 18:283-98. [PMID: 26857064 DOI: 10.1016/j.jmoldx.2015.11.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 10/19/2015] [Accepted: 11/19/2015] [Indexed: 12/30/2022] Open
Abstract
Sites that display recurrent, aberrant DNA methylation in cancer represent potential biomarkers for screening and diagnostics. Previously, we identified hypermethylation at the ZNF154 CpG island in 15 solid epithelial tumor types from 13 different organs. In this study, we measure the magnitude and pattern of differential methylation of this region across colon, lung, breast, stomach, and endometrial tumor samples using next-generation bisulfite amplicon sequencing. We found that all tumor types and subtypes are hypermethylated at this locus compared with normal tissue. To evaluate this site as a possible pan-cancer marker, we compare the ability of several sequence analysis methods to distinguish the five tumor types (184 tumor samples) from normal tissue samples (n = 34). The classification performance for the strongest method, measured by the area under (the receiver operating characteristic) curve (AUC), is 0.96, close to a perfect value of 1. Furthermore, in a computational simulation of circulating tumor DNA, we were able to detect limited amounts of tumor DNA diluted with normal DNA: 1% tumor DNA in 99% normal DNA yields AUCs of up to 0.79. Our findings suggest that hypermethylation of the ZNF154 CpG island is a relevant biomarker for identifying solid tumor DNA and may have utility as a generalizable biomarker for circulating tumor DNA.
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47
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Liu L, Yang X. Implication of Reprimo and hMLH1 gene methylation in early diagnosis of gastric carcinoma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:14977-14982. [PMID: 26823831 PMCID: PMC4713617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 10/21/2015] [Indexed: 06/05/2023]
Abstract
DNA methylation has been recently recognized as a novel tumor marker. This study investigated the methylation status of Reprimo and hMLH1 gene in both plasma and tissue samples from gastric cancer patients, in an attempt to investigate their diagnostic implications in gastric cancer. A total of 180 tissue and plasma samples (including 50 cases of gastric cancer, 50 dysplasia, 50 chronic atrophic gastritis with intestinal metaplasia and 30 normal controls) were collected for detecting DNA methylation status of Reprimo and hMLH1 genes using MSP method. Tissue protein expression levels were further tested by immunohistochemical (IHC) staining. The positive rate of DNA methylation rate was, in ascending sequence, gastritis tissue, dysplasia tissue and gastric carcinoma tissue. All those tissues had significantly elevated DNA methylation level compared to normal group (P < 0.05). Expression level of Reprimo and hMLH1 proteins were, however, decreased in pathological tissues compared to normal ones (P < 0.05). A significantly negative relationship existed between protein level and promoter region methylation level. The DNA methylation occurred in promoter regions of both Reprimo and hMLH1 genes depressed the protein expression, and may participate in the occurrence and progression and gastric cancer. The combined assay of serum Reprimo and hMLH1 DNA methylation levels thus had critical importance in the early diagnosis and gastric cancer.
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Affiliation(s)
- Lianhua Liu
- Department of Radiotherapy, Lin-Yi Cancer HospitalLinyi 276001, Shangdong, China
| | - Xiaofeng Yang
- Department of Emergency Surgery, Lin-Yi People’s HospitalLinyi 276001, Shandong, China
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48
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Jankowska AM, Millward CL, Caldwell CW. The potential of DNA modifications as biomarkers and therapeutic targets in oncology. Expert Rev Mol Diagn 2015; 15:1325-37. [PMID: 26394702 DOI: 10.1586/14737159.2015.1084229] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Knowledge of epigenetic alterations in cancer is rapidly increasing due to the development of genome-wide techniques for their identification. DNA methylation is the best understood epigenetic adaptation and disease-specific aberrant DNA methylation is a well-recognized hallmark of cancer. Recently, novel modifications, including 5-hydroxymethylation have been described, adding a new layer of complexity to understanding the epigenetic machinery and their role in cancer. There have been significant advances in techniques for the discovery and validation of DNA methylation- and hydroxymethylation-based biomarkers, each with its own advantages and limitations. With the advent of new profiling technologies, the ever-growing list of genes that show epigenetic alterations, particularly DNA methylation, emphasizes the role of these changes for early detection, diagnosis, prognosis, and prediction of response to therapies. While there are yet many challenges to the effective implementation of DNA-methylation/hydroxymethylation-based biomarkers and epigenetic therapeutics, the field is moving closer to the goal of defining personalized medicine.
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Affiliation(s)
- Anna M Jankowska
- a Lilly Research Laboratories, Eli Lilly and Company Corporate Center, Indianapolis, IN 46285 USA
| | - Carl L Millward
- a Lilly Research Laboratories, Eli Lilly and Company Corporate Center, Indianapolis, IN 46285 USA
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49
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Balgkouranidou I, Matthaios D, Karayiannakis A, Bolanaki H, Michailidis P, Xenidis N, Amarantidis K, Chelis L, Trypsianis G, Chatzaki E, Lianidou ES, Kakolyris S. Prognostic role of APC and RASSF1A promoter methylation status in cell free circulating DNA of operable gastric cancer patients. Mutat Res 2015; 778:46-51. [PMID: 26073472 DOI: 10.1016/j.mrfmmm.2015.05.002] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Revised: 04/18/2015] [Accepted: 05/09/2015] [Indexed: 12/12/2022]
Abstract
Gastric carcinogenesis is a multistep process including not only genetic mutations but also epigenetic alterations. The best known and more frequent epigenetic alteration is DNA methylation affecting tumor suppressor genes that may be involved in various carcinogenetic pathways. The aim of the present study was to investigate the methylation status of APC promoter 1A and RASSF1A promoter in cell free DNA of operable gastric cancer patients. Using methylation specific PCR, we examined the methylation status of APC promoter 1A and RASSF1A promoter in 73 blood samples obtained from patients with gastric cancer. APC and RASSF1A promoters were found to be methylated in 61 (83.6%) and 50 (68.5%) of the 73 gastric cancer samples examined, but in none of the healthy control samples (p < 0.001). A significant association between methylated RASSF1A promoter status and lymph node positivity was observed (p = 0.005). Additionally, a significant correlation between a methylated APC promoter and elevated CEA (p = 0.033) as well as CA-19.9 (p = 0.032) levels, was noticed. The Kaplan-Meier estimates of survival, significantly favored patients with a non-methylated APC promoter status (p = 0.008). No other significant correlations between APC and RASSF1A methylation status and different tumor variables examined was observed. Serum RASSF1A and APC promoter hypermethylation is a frequent epigenetic event in patients with early operable gastric cancer. The observed correlations between APC promoter methylation status and survival as well as between a hypermethylated RASSF1A promoter and nodal positivity may be indicative of a prognostic role for those genes in early operable gastric cancer. Additional studies, in a larger cohort of patients are required to further explore whether these findings could serve as potential molecular biomarkers of survival and/or response to specific treatments.
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Affiliation(s)
- I Balgkouranidou
- Department of Medical Oncology, Medical School, Democritus University of Thrace, Greece.
| | - D Matthaios
- Department of Medical Oncology, Medical School, Democritus University of Thrace, Greece
| | - A Karayiannakis
- Second Department of Surgery, Medical School, Democritus University of Thrace, Greece
| | - H Bolanaki
- Second Department of Surgery, Medical School, Democritus University of Thrace, Greece
| | - P Michailidis
- Department of Medical Oncology, Medical School, Democritus University of Thrace, Greece
| | - N Xenidis
- Department of Medical Oncology, Medical School, Democritus University of Thrace, Greece
| | - K Amarantidis
- Department of Medical Oncology, Medical School, Democritus University of Thrace, Greece
| | - L Chelis
- Department of Medical Oncology, Medical School, Democritus University of Thrace, Greece
| | - G Trypsianis
- Laboratory of Statistics, Medical School, Democritus University of Thrace, Greece
| | - E Chatzaki
- Department of Pharmacology, Medical School, Democritus University of Thrace, Greece
| | - E S Lianidou
- Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, Greece
| | - S Kakolyris
- Department of Medical Oncology, Medical School, Democritus University of Thrace, Greece
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50
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Detection of SNCA and FBN1 methylation in the stool as a biomarker for colorectal cancer. DISEASE MARKERS 2015; 2015:657570. [PMID: 25802477 PMCID: PMC4353443 DOI: 10.1155/2015/657570] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 01/25/2015] [Accepted: 01/26/2015] [Indexed: 12/14/2022]
Abstract
Aim. We examined the methylation status of SNCA and FBN1 genes in patients' paired tissue and stool samples for detection of colorectal cancer (CRC). Patients and Methods. 89 DNA tissue samples (normal/cancer) and corresponding stool samples were analyzed in our study. In addition, 30 stool samples were collected as healthy controls. Results. The methylation level of those samples was measured by methylation-specific polymerase chain reaction (MSP). The result shows that compared with the paired controls, both SNCA and FBN1 were significantly hypermethylated in CRC patients in tissue samples (P < 0.001). In the stool samples, hypermethylated SNCA and FBN1 were detected to be significantly higher than that in normal stool samples (P < 0.001). The combined sensitivity of at least one positive among the two markers in stool samples was 84.3%, with a specificity of 93.3%. In addition, our experiment suggested that the positive rates of SNCA and FBN1 in Dukes A stage were significantly higher than that of FOBT (P = 0.039; P = 0.006, resp.). Conclusion. We concluded that methylation testing of SNCA and FBN1 genes in stool sample may offer a good alternative in a simple, promising, and noninvasive detection of colorectal cancer.
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